Google Analytics has a Query Explorer which can be used to troubleshoot your Google Analytics data source.
1. Make sure you are logged in to the Google account that has access to the Analytics property and select it.
2. Select these parameters in the form:
start date and end date, choose the date for the period where you see a mismatch
metrics, choose the metrics where you see the discrepancy
dimensions, (important to choose date and all the dimensions you have in your Funnel data source)
To find out which dimensions that are included in your data source, you can see an overview under the definition label in the data source details page in Funnel. If the list is too long to view you can check the "Edit Configuration" window.
3. Final step, scroll down and click "Make request" button. The result can be viewed as a table or as JSON and you can use that result to compare them to your Data Explorer in Funnel. Comparing the values is done row by row to the rows in Funnel data explorer.