Yes, I am sure they had to disconnect the tranny cooler lines to remove the engine. So the swap could be tied to it if they did not refill the tranny properly. But it could just be some pretty rotten luck...hope not and they make it right. Are you throwing any codes or is the tranny light coming on?
I just got done buttoning up my tranny tonight. I have been leaking bad for a while. I dropped the pan, since I was in there changed the filter, new gasket and filled it with fresh fluid including a bottle of Lucas stop slip. Left the skids off for the night to see if anything leaks. Also scrubed the pan...first time it has ever been silver! Had all kinds of fluid burned on to it.