Having beaten Middlesbrough at the Riverside with Ryan Taylor playing up front alone, the Scot decided not to change his tactics so forwards Sam Baldock and Steven Davies started on the bench.
And after the visitors romped to a comfortable win to leave City winless at Ashton Gate since August, McInnes stood by his selection.
“Performances like that leave you open to criticism about your formation and tactics – that is par for the course,” he told the Bristol Evening Post.
“But no-one was complaining about us playing one up front when we got the draw against Blackpool and when we beat Middlesbrough.
“Let’s not be kidded; playing with two strikers would not have made a difference to the goals we are losing.
“We were poor defensively and we were out-muscled and out-fought a lot of times at the back. Playing with two strikers would not have helped that.
“That was the type of performance that gives everyone a platform to criticise us. There is absolutely no question about that. It is difficult and I totally understand the frustration on the part of the fans.”
Fulham manager Slavisa Jokanovic believes his team's win at Sheffield Wednesday was a 'crucial moment' in the race for promotion to the Premier League.
Sunderland missed a glorious opportunity to boost their slim Sky Bet Championship survival hopes after drawing 1-1 with 10-man Leeds at Elland Road.
Aleksandar Mitrovic fired Fulham to a priceless three points as their automatic promotion hopes were boosted by a 1-0 win over Sheffield Wednesday at Hillsborou