There are several reasons why so many practices loose an audit with a Medical Records system. 

In our audits unfortunately we find most practices using an EHR system would fail an audit.  

Stage 1, 2, ... Certification Does Not Indicate Compliant Examination Documentation

Many doctors assume their EHR system is compliant because it has met Meaningful Use Certification (MU).  MU is not the same as compliant examination documentation.  Many "Certified" systems have failed Insurance audits because they are not compliant and missing many required examination elements..

EHR System Missing Required Exam Elements

Some systems simply do not contain the information required for compliant exams.  In many cases where a practice has failed an insurance audit, the auditor has told the practice to contact the vendor to fix the problems.  For years we have discussed non-compliant exam documentation directly with the vendors.  In several cases they have chosen not to make the necessary changes for compliance.

EHR System Not Verifying Your Documentation

Several EHR systems have a process to verify that the exam documentation is full and compliant.  In many cases this verification is not accurate.  We have seen multiple cases with many systems where exams were "verified" compliant by the EHR system but completely missing major required elements of the exam.

Modifying Exam Templates

Frequently we see compliant EHR systems made non-compliant by the changes a practice makes in their templates.  History, Exam Elements or other required information are deleted or not carried over in new templates. This renders the exam non-compliant.

Exam Printouts Missing Information

When you are audited or have a request for records the auditors want a printout of the records.  We have seen in the majority of EHR systems, where information that has been reported and is displayed on the EHR screens is not in the print out.  We have seen practices loose an audit only because of this "missing" information. 

EHR Vendors' Response

We have discussed these and other issues with most of the EHR system vendors.  In some cases they try to get the issues fixed.  However, in too many cases they deny it is a problem.  In discussions with several of the vendors: I asked:

I asked: Why does your system not warn the user when required information is missing.

Their answer:  "It is the users responsibility!" 

My comment to them is:  Isn't the purpose of an EHR system to make sure they are compliant?

Their response:  "It's the users responsibility!" 

No that is the vendor's responsibility!