Are there instances in which Tag Assistant won’t pick up tags?

If you enable 'Parse External Scripts’ in the User Settings -- no. 
If you’re using the default version and have not enabled checks for 'Parse External Scripts' -- yes. If the Google tag is implemented incorrectly such that the pixel itself does not fire AND the tag is inside of a container tag, separate script, or iFrame, the Tag Assistant will not properly diagnose the implementation. This is a very small subset of scripts that we are working on a resolution for. The issue is that the primary check, header checks, will not detect scripts that do not fire. The secondary check, source code lookup, does not detect tags implemented inside of containers or iFrames.