If the pipe didn't leak before your repair I think it's unlikely it was damaged during your repair. How old is it and your boat?
When the engine is running the exhaust blows most standing water out. With engine off the water level rises to the boat's waterline and the pipe fills above this joint.
Unfortunately any repair is going to take another engine pull. Then you can first check the torque on the transom joint. If it is loose, particularly on the top fasteners, water could be oozing out the top. The rubber seal in the transom plate doesn't set out much from the transom plate surface. It mashes flush with the joint when torqued up. If missing, or if you didn't replace the original it could leak.
Also the transom must be parallel inside on out. If it is not, the alignment with the exhaust manifolds could be off enough to put a downward force on the pipe joint.