Can we change jersey numbers in the game? For some reason I have multiple players with the same jersey #.

Go into Commissioner mode, select edit players/recruits, then select your team and the player(s) whose number you want to change. I also turn on the "see bio only" toggle so that I don't see the actual ratings of the players.

Thanks - and then my next question is shouldn't the game not be doing this and only assigning jersey numbers that are available?

Have you installed the most recent update to the game? Version 10.1 should have corrected this issue.

I still saw it happen even after 10.1.

I have the newest version and def have seen it.