The Seagulls' goals both came from set pieces and the defeat dropped McInnes' side into the Championship relegation places.
"The Championship is an unforgiving league and if you don't defend set-plays you're in trouble," he said.
"The first goal came from a free header and the second was a breakdown in communication between Matthew Bates and the keeper.
"Yet I believe that had we got one back, Brighton would have been more fragile. We kept going but for all our good play in possession we couldn't get anything from it.
"We needed to get the ball forward a little bit quicker, but I thought we worked hard against the ball."
City have now lost 10 of their last 14 games, to drop into the bottom three, but McInnes is optimistic his men can climb away from trouble.
He said: "We've played Blackpool, Middlesbrough and Brighton in our last three games and they have been tough ones. Our league position is of concern, but I firmly believe we will be all right.
"We have the belief, we didn't buckle and we were always in the game. We needed a goal to make Brighton anxious."