Greg Pearson appeared to have fired Burton into the lead in the 30th minute, only for the referee to pull play back to give a penalty for an earlier challenge by Andy Gallinagh, who was sent off as a result.
To add insult to injury, Pearson netted the resulting spot-kick before Jacques Maghoma wrapped up the points for Albion.
Yates said: "I can't say too much because I can't afford to pay an FA fine. But the referee has had two big calls, I've seen the DVD of both of them and I think he's got them both wrong.
"Their first goal may have been bad defending for letting the play in, but it wasn't a penalty. Andy Gallinagh got something on the ball.
"The ref has blown before the ball has crossed the line and he's realised he's made a mistake - so he's given a penalty and sent a player off to punish us twice."
Source: PA
Source: PA