There are 2 Save buttons, one under Off/Def and the other below the Practice Minutes. Make sure your clicking the right one. The upper button only saves the Off/Def minutes.

The worst is when you change your team minutes and don't save them, then go and do all of your individual minutes and it won't let you save those because you didn't save your team one. Then you save your team one and all your changes to the individual ones erase.

That has always been a tiny little nuance that turned into a huge pet peeve of mine in this game only becuase I forget so frequently.