How would you fix this leak?

The contractor that installed this trophy drain in the standup shower, cut the ends off to modify the length. Unfortunately, they weren’t able to get a good seal on the ends and water is leaking down past the waterproofing and into the ceiling below.
What would you do to fix it? Caulking only held about nine months or less. I was thinking of using a fiberglass resin to plug the holes. What would you do?