If you are intent on running 3 TE sets there's a rather time consuming way to make sure this doesn't happen. Put 3 players in your TE depth chart, the 3 players you would like to block on those plays as a TE (your starting TE and 2 WR's for example). Then, put your starting TE as the TE1 and make sure in your Advanced AI that every play that isn't that 3TE run is set to TE1.
What this will do is make sure your RB is at RB when the 3TE set comes in because the depth chart now has 3 players to play the TE spot in the DC, and it also makes sure that only your starting TE is the TE during all your other plays. But, you HAVE to make sure to set both. One or the other will just mess things up further and you'll either fix nothing or have WR's playing TE.
Or you could just sign 2 more TE's, but that would make things more difficult for PT and whatnot.