missing module debuggin

Hello, this might be a vague post, but will try my best.

I have a situation where we have one code base and multiple dev and test environment.

I am in a situation where the developers are claiming a particular heavily customized module function is displaying on one environment but not in the other. 

I checked and double checked and I am pulling the correct code from the correct git repo.

I also checked apache permissions and file and folder permissions. They seem all correct.

I cleared and re-cleared drupal caches

My question is, is there a to debug exactly from which php file and which mysql entry does a module get driven from? 

The developers dont seem to know. All they can tell me its working in one environment and not the other.

Drupal version: 

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