They also do a lot of sounding/ testing of the ground where they are planning to put in a coaster so they don't randomly drop a support into a cave and risk collapse- of either the tunnel or the support/ coaster. Even with all of the coasters around SDC they've been careful and sure to not build over any caverns that they know of.
I hadn't heard that they actually filled in a cave opening, but it's possible. What I heard was that it took a lot more cement to shore up the hill side than they expected and that's where a lot of the cost went. Time Traveler should have been far enough away from the cave that it shouldn't have been a problem, but it's easily possible they found a small one when doing the ground testing and checks and had to work on it some.