I had a player this season who was a sophomore after being ineligible his freshman year, he was clearly at the bottom of my roster talent wise.  He complained about minutes once, never mentioned transferring in his complaint message.  Then at the end of the season he leaves, is there any way I could have seen that coming so I don't have it happen again?

It's always a risk, albeit a small one.   I don't know of any warning messages that will tip you off.  

Whenever I have a complaint, I make sure I meet their request.