I think it is possible the crater could have been caused by a missile from Galbadia. I mean, earlier in the game the team goes to the missle base, messes around with the coordinates and then leaves.

Quite a number of missiles got fired per target (as we see in the FMV) - then compare the massive crater left where Balamb was and the crater in Trabia; perhaps the "fiddled" coordiantes led to some missiles hitting Trabia Garden and others straying to where the crater is.

Doesn't explain why the Ragnarok is repelled from it though . . .