yeah we have been working to identify the issue. What I have uncovered is that if you flick down on teh right stick, while controlling any player it will trigger a run commit. People who control secondary or linebacker don't typically see this, but those who control DL do because of the "User Jump Snap" technique. User jump snap has been removed from Madden, so as long as you wait til after the ball is snapped to use the RS, you won't have a problem.
More info, this on Auto-Subs/Fatigue. Kinda sucks for people that want to use 2 back systems or get their backups some decent snaps, especially since progression is solely tied to production. http://www.operationsports.com/forums/madden-nfl-football/571567-fatigue-auto-sub-discussion.html
He said he's playing offline, where the sliders are fucked. I've had no issues getting my backup HB tons of touches in online CCM
Don't pay attention to the yellow slider bars. You have to set the fatigue level for sub in and sub out. The yellow bars will trow you off because it looks like a push/pull but it works exactly the same as NCAA auto-subs.