The biggest flaw is that it takes 2 seconds to adjust their depth chart position before doing training, and then putting back to normal before a game.
As example if I am the Texans and have Vince Wilfork as my starting DT and DJ Reader as his backup. I can simply move Reader to the starting spot, run the drills, then move Wilfork back into the starting spot.
Workaround is too easy that it ruins aspects of the game. The system as a whole has lots of flaws. For example if you run a 3-4 system, adjust the position of your starting DEs to OLB. Now run a defensive drill that gives XP to LB/DB they only player not getting XP should be your Defensive Tackle. (Likewise if you run a 4-3 move your OLBs down to DE and run a DL/DB drill leaving only the MLB without XP). (You can also do the same with TE/FB easily).
As a note if you are playing a league on your own, you obviously don't need to abuse the system if you don't want to, however if you are in an online league others might be using these tactics to their advantage (depending on how much the commish pays attention) and you might be getting left behind.