You're talking about the HB (or any other player, it's definitely not just limited to HB's) not re-entering the game late in the game, right?
That's not a bug, it's the progressive fatigue and auto-sub systems playing off of each other. When people jack the Autosub In setting way up, that raises the energy threshold a player has to reach during recovery to re-enter the game. Set it high enough, with the fatigue effect increased....and they'll never reach that threshold, and never re-enter the game.
I get that people don't like how it works (I can't say I disagree with that opinion) but regardless, that
is how it works, and it's not a bug.