1. Check league import issues
Go to Edit All My Leagues (found on the more menu in mobile apps). For the league concerned, hit Details > League Import Issues. Make sure to read this carefully as it will report any incompatibilities between your league and Footballguys. While we have the widest support of any fantasy site, and will aim to support any rule that 5% of our users' leagues contains, it may be there is an aspect of your league that is not supported and is reported here.
This is usually related to scoring; in which case you can manually enter your scoring - see the next section...
2. Check your scoring and manually override it
Go to Edit All My Leagues (found on the more menu in mobile apps). For the league concerned, hit Details > Scoring.
Carefully check this against your league. Anything that isn't exactly the same as your league should have been reported to you in the League Import Issues in step 1.
A good example of this is leagues that only award points for yardage based on lots and lots of split out categories, or only award points for combined yardage (ie, rushing and passing yards added together, rather than calculated individually).
If you believe that scoring is the explanation for the strange rankings, scroll to the bottom of the screen that reports the scoring that was imported and hit "Manually Enter Scoring".
Then, use the form there to enter the scoring for your league.