Hey there,
Sorry to hear about your loss of players. I have had it happen a few times on Madden Mobile but after I contacted support they were able to find out where they went. A lot of times, for me personally I end up adding people to sets before i set a new lineup and because i go through my game so quickly just to get sets done.
I would suggest contacting phone support so they can review the account itself and see why they went missing and where they went. They will be able to tell you if they were sold or added to a set etc.
http://help.ea.com/en/contact-us/new/