This is how IR players in roster updates have always been handled; a team's roster in Madden can only handle 55 players (53 + one created player + one for Superstar mode), and the concept of a dedicated injured reserve does not exist in Madden. As such, players who get injured are removed from the roster file entirely; for example, John Phillips, a tight end for the Dallas Cowboys, was removed in an early roster update because he tore up his knee and went on IR.
Frankly, I'd rather see the injured players end up in the free agent pool in the meantime. Ultimately, Madden NEEDS to add a working and fully-functional injured reserve list to the game.