Steven Fletcher looked to have been taken out by Adam Nemec as the striker tried to run on to a loose ball deep in Slovakia’s half.
Play was allowed to continue with the hosts quickly moving down the right. When Marek Hamšík’s back post header was pushed back into the centre of the penalty box by David Marshall, Róbert Mak slammed the ball home.
Strachan admitted he was surprised the referee did not spot the foul on Fletcher.
He said: “That was perplexing. I’m wondering how he can’t see that.
“That didn’t help us, that’s for sure. We’re needing that wee break now and then.
“We’re one point away from a play-off place at this moment. What we’ve got to do is find the right system to play the next game.
“We don’t usually tinker with it to much. We had an extra midfield player tonight which we felt worked for a long period of the game.
“We will just have to look at it again.”