Check league import issues
Go to More > Edit All My Leagues. 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 will be reported here.
This is usually related to scoring; in which case you can manually enter your scoring - see the next section...
Check your scoring and manually override it
Go to More > Edit All My Leagues. 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 (e.g.: 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.
Check keepers
Missing players can sometimes be explained by keepers. Sometimes leagues are in a strange state where a commissioner has not cleared out rosters from the previous year. In this case, we may assume those players are keepers.
Go to Draft Settings > Keepers. Check that all players listed for each team are actually keepers, and use the X button to remove those that aren't.
Check player pool filters
If keepers did not explain missing players, this is almost certainly the explanation!
Go to Draft Settings > Player Pool Filters. Check that no teams, conferences or divisions are incorrectly excluded from the player pool here. If they are, move all the toggles across to the left, to disable removing these players from the draft pool.
Last resort for incompatible leagues
Some leagues have setups that are so advanced, the best option is to create the league manually instead. While this will apply to very few leagues, one example might be a league that uses team place kickers, which is not supported by the Draft Dominator at this time.
On phones, go to the Draft tab and hit New Draft at the top. On other devices, hit the Switch Draft menu option then hit New Draft.
Now, hit the Add Leagues button. Scroll past the options of importing from all the different hosts. Underneath is a text box. Enter a name for your league here and hit "add".
Then, add a draft to this league.
Then use the Draft Settings menu to set up your league using the same interfaces that were required to set up all leagues in the app in previous years.