David Lopez was clumsily bundled over by Rovers substitute David Goodwillie in the box when five additional minutes had elapsed and the Spaniard picked himself up to convert the resulting penalty.
The former Portsmouth and Blackpool boss then heard fourth official Peter Wright urging Robert Madley to blow for full-time moments before the decisive incident occurred.
"The most disappointing thing - I've got to be careful what I say a little bit - is for 45 seconds the fourth official is screaming down his mic to the referee 'that it's, it's done, it's finished'," Appleton explained.
"So to concede after that is disappointing. Having said that, it was a silly challenge from David - he knows that - and it's cost us."
Scotland international striker Jordan Rhodes, one of the few success stories of a turbulent campaign at Ewood Park, netted a fifth goal in as many league matches with a spot-kick of his own to hand Blackburn a slender advantage on the stroke of half-time - just reward for a gameplan Appleton felt worked to perfection.
"We did look comfortable - that's the most disappointing thing," he added. "We controlled the game in terms of we knew exactly how Brighton play - there was a gameplan in terms of how we would set up and how we would deal with it.
"Their keeper was certainly a lot more busy than our goalkeeper on the night. I think if we'd have got the second goal we'd have won the game comfortably."