Missing one of your Perfect Team cards? See here.
 

Under some circumstances it may happen that a player you bought / won in an auction / pulled from a pack may disappear after the latest league file got downloaded.

To fix this, go to the Main Menu -> Manage Cards, the missing player(s) will be listed there as inactive (if not, restart OOTP, then they will be). Click on "activate" next to them, that will place them on your reserve roster. Then submit your team.

Hope that helps! :)
Markus