If you are referring to the process of application and accreditation assessment, typical gaps include:
Method Validations not extensive enough
Internal auditing program not fully established
Reporting of results not compliant
Internal and External (PT Scheme) Quality checks not sufficient
Ineffective handling of Nonconformances and corrective action.
These often arise due to organisational structure issues; where responsibilities and authorities are not clear and personnel do not understand the true intention of the QMS, purpose of ISO 17025, how the various activities link and how to take a risk based approach to decision making.