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My number 1 question is how can the liner of the shower get filled with water? Again, how does water even get in the pan?
If I had to lay blame I would lay it on the tile man. Let me explain. Water will seep between the tile grout and down through the mortar when the shower's in use. This is why weep holes are in the base of your flange type shower drain,(see image). The weep holes allow the water that seeps down to drain back into the trap. If the tile man allows mortar to get in the weep holes and seal them off any water that seeps down will build up and leak out. Hope this helps, Tom