When I transfer players out of my reserve team, the game bugs out and leaves them in. There is a similar bug when I transfer players from other team's reserve teams, they can still play for both teams.

 

For example, as Hertha Berlin, I moved Ibisevic to my reserve team, then later swapped him with a player I wanted. He still shows up in-game as in Hertha BSC II (which I can't view in FMRTE).

I also (in a separate move) transferred in Fiete Arp from Bayern II; he still plays for Bayern II while also playing for me (and will often show up as ineligible due to 2 matches on the same day.)

That doesn't sound good 

Read this thread if running app as suggested report as a bug

 

I have the exact same issue and was unablr to solve it. Tried to deleted other squad reg but nothing... ☹️

Follow the advice given above mate

 

also in game have either of you made sure the said players are not available to play for the reserves you can do this without using FMRTE