The Dons held on for a goalless draw to make in three matches unbeaten, but for the third game in a row the team looked completely out-of-sorts.
McInnes tinkered with the line-up and formation once more, but his changes once again failed to lead to a cohesive team performance.
And fans are now questioning some of the manager's decisions, such as recalling Jamie Langfield and Willo Flood, and Kenny McLean's continued selection.
Mcinnes said: "I felt we were dominated in the first 20 minutes of the game and we were unlucky not to score in that opening minutes.
"However, we were quite poor today. It is quite out of character for us."
Thistle changed their formation in the 31st minute after Kris Doolan came off for Lyle Taylor and McInnes accepted his side struggled to adapt.
He said: "After they changed formation, I felt they caused us significant problems attacking and we never challenged them enough. I think it was a poor performance.
It was a bad day for us and we were lucky enough to take a point from the game."
Aberdeen take on third-place Inverness on Wednesday with the chance to move 11 points clear of their nearest challengers, all but securing second place in the SPFL.
McInnes added: "We need to make sure that we finish the season strong. Our aim is to finish at least second. We aim to improve after every match and intend to do so for Wednesday."