Patient Conditions Lost in Templates: How EMR Documentation Can Trigger Billing Discrepancy

A chart auditor opens a provider’s note for a two-week follow-up encounter after a course of antibiotics for a sinus infection. The documentation in the electronic health record includes a complete 14-system review of systems (ROS), comprehensive exam findings across multiple body systems, and an assessment copied forward from the previous visit. The note spans multiple pages and appears thorough at first glance. However, as the auditor reads through, it becomes impossible to determine what actually occurred during the encounter, such as what the patient reported, what the provider assessed, or what clinical decisions were made. All of which creates a significant red flag regarding documentation practices.

When auditors consistently encounter this pattern across a provider’s charts, it signals that EMR templates designed for thoroughness and efficiency are increasing compliance risk and unnecessary documentation burden.

Why E/M Documentation Compliance Matters More Than Ever

With increased payer scrutiny, expanded use of data analytics, and AI-assisted coding tools, documentation that fails to clearly support medical necessity is more vulnerable than ever. Auditors are looking for relevance, clarity, and clinical rationale.

For organizations, poor E/M documentation can lead to:

• Overpayment demands and recoupments
• Increased audit frequency
• Compliance exposure tied to overcoding
• Provider frustration and documentation fatigue

What Changed That EMR Templates Missed

The 2021 and 2023 evaluation and management (E/M) guideline updates fundamentally shifted visit level selection to medical decision making (MDM) or total time, except emergency department visits, which use MDM only.  Extensive history and exam components in the electronic medical record are no longer required. Instead, guidelines allow “medically appropriate history and/or physical examination” at the treating provider’s discretion.

Yet most EMR templates still prompt for, or even require:

• Complete review of systems (when only pertinent systems are needed)
• Comprehensive past/family/social history (no longer used in level selection)
• Detailed or comprehensive exams (which may not be medically necessary)

This creates a false sense among providers that more documentation equals compliant documentation, when the use of outdated templates create different compliance risks.

Template-Driven vs. Story-Based Documentation: A Real Example

Compare these approaches for the same sinus infection follow-up:

Template-driven Documentation

"Follow-up recheck of sinus infection. 14-system ROS negative except as noted. Constitutional: fever resolved. ENT: congestion improved. Respiratory: no SOB. Cardiovascular: no chest pain. GI: no nausea or diarrhea..." [continues with detailed exam]

Story-based Documentation

"Patient reports fever resolved after second day on Z-pack. Sinus and nasal congestion improved considerably with no sinus pressure. Still experiencing some nighttime post-nasal drip causing minor cough. No GI symptoms or other side effects from Z-pack."

Which one tells you what happened in today’s encounter?

The Habits Outdated Templates Create

When templates demand comprehensive documentation, providers may rely on documentation shortcuts. This may include overly templated content, or excessive copy/paste that brings forward old content without updating with today's assessment. This “note bloat” practice obscures the clinical decision-making that other health care providers and auditors need to see. 

Common issues when over documenting is based on template prompts:

• Non-pertinent 14-system ROS across multiple encounters
• Comprehensive exams unsupported by the chief complaint
• Multiple diagnostics carried forward without clarity of pertinence
• Overcoding risk when documentation volume exceeds medical necessity

Every other clinician involved in the care of the patient needs to glean accurate and up to date information in a short amount of time. The continuity and quality of care depend on it. 

The AI Complication: When Technology Enables Overcoding and Over-Documentation

Here’s where things get more problematic. As EMR systems deploy AI-powered coding tools, these may compound the problem by suggesting higher E/M levels based on content alone, without the reasoning and rationale of selecting only the elements that were clinically relevant.  

Consider that sinus infection follow-up patient encounter with comprehensive 14-system ROS, detailed multi-system exam, and lengthy copied-forward problem list. An AI coding tool might suggest a level four (99204/99214) based on documentation volume and its inferred “complexity.”

What AI misses, that most human auditors won't, is the disconnect between documentation and medical necessity. A straightforward follow-up clinically warranting a level two (99202/99212) or level three (99203/99213) now looks like potential upcoding because templates generated documentation exceeding what the patient's condition required.

This creates a new vulnerability: AI-assisted overcoding driven by templated note bloat from EMR templates. Your documentation may pass automated review initially, but targeted audits focusing on medical necessity will identify the mismatch. The result? Overpayment demands, compliance scrutiny, and defending services beyond what the clinical picture supported.

We are not implying that the solution is always less documentation. What we are saying is that the goal should always be relevant individualized documentation that matches clinical necessity. Remember: medical necessity is the overarching criterion for payment. 

What Modern Patient Care E/M Documentation Should Look Like

Post-2021 documentation should tell today’s story through a history that captures the context of the patient’s presenting problem(s) and a relevant exam that provides objective information, ideally leading to meaningful data being ordered or reviewed. This should lead to a greater sense of clarity in how the provider reached the associated assessment and plan which should highlight the cognitive efforts of the MDM with:

• Clear problem assessments showing today's status
• Data reviewed or ordered with clinical rationale
• Documented risk and patient management options considered and/or selected

Remove the unnecessary: 

• Complete ROS unless clinically indicated
• Comprehensive PFSH unless relevant to today's care
• Detailed exam elements beyond what's medically necessary 

Even when leveling by total time, documenting the patient’s clinical story remains vital for supporting medical necessity. Time documentation must be near exact and include a description of the activities performed during the time reported. Avoid templated time statements that read alike across multiple patients and include outdated language like "greater than 50% of the time..." which doesn't reflect current guidelines.  

Action Steps to Take Now

For Providers: Read through your last five (5) notes and honestly answer the question: would someone reading them understand what happened today? What problems were assessed, which data elements informed, and what is the management plan? 

Challenge your template defaults. If the template auto-populates data, ask yourself if it’s relevant to today’s encounter. Spend your documentation time on what matters: cognitive work associated with problem assessment, data analysis, and risk associated with patient management options. 

For Practice Administrators: Conduct a template audit against current E/M guidelines. Identify what your EMR is requiring that the guidelines do not. Invest in provider education on the current E/M guidelines and partner with your EMR vendor to modernize templates. 

A few quick wins to consider in template revisions include: 
 

Old Templates Prompts	Modern Template Should Ask
Complete 14-system ROS	"Any additional symptoms related to presenting problem?"
Comprehensive exam checkboxes	Focused exam based on chief complaint
Quarterly PFSH update	"Any changes affecting today's care?"

 

The Bottom Line

Your templates should support compliant documentation, not generate sheer volume of non-pertinent information. Modernizing your approach means less time documenting, a clearer clinical story, and better audit outcomes. 

It could also result in higher quality of care and clinical continuity by simply creating an easier to read note that allows other clinicians and care team members to know exactly what is going on with the patient in far less time. 

How RubinBrown Can Help 

Modernizing E/M documentation isn’t about replacing your EMR; it’s about aligning workflows with current guidelines and clinical reality.

RubinBrown helps organizations by:

• Reviewing documentation patterns to identify where templates create unnecessary risk
• Clarifying guideline expectations for providers
• Assist with refining templates and workflows to reduce burden and improve accuracy
• Strengthening audit readiness by ensuring documentation consistently supports medical necessity

Our goal is to help you create documentation processes that are clear, compliant, and sustainable, allowing providers to spend less time documenting and more time caring for patients.
 

Published: 02/20/2026

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