Its normally out of contract players/unsigned players that leave gaps. Not looked at the days of your post or game but ultimately this is rectified when 7 days have elapsed since the Season started - when the players are released and the system realligns the squad positions with the 'filler' players it already added on day 1. So if the match was still in the first week there's your answer.
Not sure if you can also force the system to use out of contract players through Saved Formations - never tried it, but I doubt it.