I wouldn't touch anything and I wouldn't tell them what you saw, or that you even looked. Take pictures of what you can see and keep them to yourself. Then take it in and tell them what the issues are. If it still does it after you get it back, or if they tell you they didn't find anything, you can ask them about the loose clamp and hanger that isn't installed. Chances are that they pulled the trans to fix it and that required exhaust removal. They botched putting the exhaust back on. It happens from time to time, especially if they have one guy that starts the job and he has an apprentice or helper that finishes up the loose ends that he took apart. How they respond to the issue is a bigger deal than the issue in most cases.
I would be interested to know what the code is. There's a lot of room for problems when pulling a tranny out. Could be something left unplugged, a pinched wire, or any number of things.
2012 Silver Sport S, Silver, 6 speed, soft top, 3.73s, LSD, PCG, Infiniti, deep tint windows, Pro Comp 1028 wheels, 33" Duratracs, Smittybilt bumpers and steps, KC fog lights, Mopar slush mats and fuel door.
Happiness is a belt fed weapon.