Yeah happens to me all the time, you can't even challenge the play!
Sure you can. Just hit the Start button to pause play, go to coaching options and select "challenge play". I challenge and win on fumble calls quite often and have won a couple of challenges on out of bounds plays as described by the original poster. Bad calls are a part of football and the fact that the challenge option is built into Madden is a nice feature, IMO. Of course, if you lose, you lose a time out, etc.
Note - sometimes you have to select the next play call before the "challenge play" option shows up in the coaching menu.
Actually this has happened to me multiple times. Today I was playing and Calvin Johnson clearly caught the ball in the 3rd quarter and had 3 steps in bounds and the 4th step was out in the back the end zone and it was called out of bounds. I tried challenging the play but I could not. i even picked a play called and called time out to see if it challenge was there but it never showed. I had not challenged a play before, not sure what is going on and why the play can not be challenged.