The Clarets were forced to play the final 33 minutes with 10 men after keeper Heaton was red-carded for handling the ball twice inside the area in the process of releasing it.
Dyche felt Brighton's Will Buckley had touched the ball in between the keeper touching it twice himself.
Dyche said: "Factually I think he (Sheldrake) has made the wrong decision.
"I asked the referee for his view and he said it was for unsporting behaviour, throwing the ball up in the air and catching it twice.I asked him whether he had seen our player impeded in the area.
"The referee has got one chance to look at it and he made a quick decision. Maybe had he spoken to the linesman there may have been a different outcome. The referee also said to me that, in making the decision to send Heaton off, he wasn't affected by his first-half decision not to."
This was Burnley's first defeat in five league and cup games this season and Dyche felt the sending-off "changed the second half."
"In the first half we had the upper hand and we started the second nicely on the front foot."
Dyche confessed that, in terms of controversial sending-offs that he has witnessed, Heaton's dismissal was "up there in the top five." He added wryly: "You live and learn."
Andrew Crofts and Leo Ulloa were on target for the Seagulls.
- Sports & Recreation