Billy Kee gave the hosts the lead only for Deon Burton and Niall Canavan to put the Iron in front with quickfire goals after the break.
But Robbie Weir headed the Brewers level in the 62nd minute to end a run of three successive defeats but Rowett was focusing on the away side's appraoch.
He said: "They've come here and slowed the game down and disrupted it.
"That's up to the them, but for me the officials have to take control and not allow them to do that.
"In the end, it almost spoiled the game because they never allowed us to get going after the equaliser. It's left me feeling really frustrated.
"They had five players go down at various intervals and three times the referee stopped the game to allow them to be treated for cramp.
"Nevertheless, I still believe we should have won the game and had the opportunities to do so.
"To end up being 2-1 was a disappointment and tells me we need to be more professional. It was an opportunity wasted to win a game."