David Edgar put the Clarets ahead on 55 minutes but Wanderers' substitutes Craig Davies and David Ngog both struck to turn the game on its head.
"We played some good stuff, we kept the ball and I think the frustration is the fact that after we scored we didn't keep the ball," said Dyche.
"That's our strength, using the ball and keeping the ball and we've seen that many times lately.
"That was my biggest frustration with the players and I spoke to them about that afterwards, other than the obvious which is the outcome.
"At 1-0 I thought the frustration among Bolton's fans kicked in here and if we'd have dealt with the ball better and kept it better I think that would have only grown."