When considering gaps in the implementation there are two types of issues. The first is a deficiency, where a mandatory requirement is not met. For example, external proficiency testing to meet clause 7.7.2. The second is where there is a process implemented, but it is not achieving the intended result. An example here is ineffective Management Review.
In my experience the requirements for monitoring and evaluation is often not achieved. For example all the requirements for Management Review input (clause 8.9). Another area is method validation / verification (clause 7.2), where it is often not to the extent required. Furthermore labroatories often underestimate the effort and requirements for the management of personnel (clause 6.2), equipment (clause 6.4); and quality control (clause 7.7.1 and 7.7.2) to ensure competency and validity of results.