Danny Murphy put Rovers ahead after seven minutes and Grant Hanley pounced on the hour mark as the Robins lost their second consecutive away game - they have also not won an FA Cup tie since 2007.
"It didn't feel like a proper cup tie. It was strange and I felt we've gifted Blackburn both goals but certainly the first goal is crucial," McInnes said.
"We give the ball away in an area we know we have to handle the ball well because Blackburn are a counter-attacking team and want to get you on the back foot.
"Certainly the goal they scored from, we should be dealing with. I felt second half, we made changes to freshen things up.
"We brought three substitutes on quite early but we lose a second goal from the second part of a set play and that's another gift. It's a messy goal.
"I don't think Blackburn have had to work too hard for both of their goals."