Today I was fishing a Texas rigged trick worm and got a strike and set the hook as normal but noticed the rig went in his mouth and out his gills and when I set the hook he was hooked in the side near the stomach.

So the line and hook still went through his mouth but I guess somehow fell out through his gill before I set the hook. Would this still count as foul hooked?

No that is not a foul hook, and unless you were site fishing it wouldn't matter anyway.

Here a fish has to be hooked in the mouth to be legal.

not in my opinion but i know certain states have regs that say the fish must be hooked in the mouth to be considered legal or not.

Some times the hook gets sucked through the gill when they vacuum/pick it up, I have never had a fish get hooked in the stomach in the way you described though, I always just hook gills. I wouldn't worry about it

As long as the line is going into the mouth I don't think it will be a problem.

I'm not worrying about it I was just curious, because I know if your sight fishing in a tourny foul hookups don't count.