My advice is to not compare data. These are 2 systems that have 2 very different ways of tracking, monitoring, and reporting.
I also feel that maybe "troubleshooting" and "issue" is not the right way to categorize this need as it may drive you in a direction where you think there is something wrong. You may want to just validate data in each system.
Once you can validate the data in each system, you can compare the data from a relative perspective, but know that it will never match up.
Some things to consider (definitely not all):
- Are both the scripts on the same pages?
- Are the results based on the same time constraints?
- Do you have all the factors in both systems looking at the same thing?
- Have you validated any data in any of the systems to know and use at least 1 of them as your true source of data?
All in all, are you comparing apples/apples?
^^Completely IMO so please take it with a grain of salt. Just want to nudge you in the right direction, somewhat.