1996 Honda Civic Tranny

Very doubtful. It's unusual for a cv joint to be damaged by a collapsed engine mount, but I have heard of that on Hondas before. It's more likely the inner joint isn't fully seated in the transmission. They have an internal spring that pushes the housing into the transmission and keeps it there. It can be possible to assemble the suspension parts with the inner joint not fully seated, although typically you'll have fluid leaking out there.