most likely what happend is somthing droped down the open shifter tunnel while the trans is out.
I have seen this happen to other techs a few times, and they never want to listen to the easy way to prevent this.
I use a shop rag and a rubber band , put the shop rag over the shifter opening and then put the rubber band around it so nothing can go down there.
I am sorry to hear that this happend to you, and you probally have no way of proving this since they already took the trans apart, You may want to try and file a small claim lawsuit against them and see what happens. Go in and tell the service manager that you know how this happend and your taking all the parts and having a tremec specialist look at it.
Hell they could p05 the repair for you ( this would cover most if not all of the repair under warrenty) if your car is less than 7 years old. If you can get this manager to come on here I will argue with him about it for you.