I'm sure the Dev's are aware but I've been falling through space on a few occasions of note:
1. Klingon space, when transitioning laterally through the 3 nebulas (T'Ong, D'Kel and so forth). This occurs by going to one nebula, then opening the map, and selecting the next nebula over. The ship will fly hugging the border then suddenly will glitch and fall through the map. A ducttape fix is to fly back toward the center of the Omega L system while flying down, or to transwarp to another location.
2. Hormi(sp) Cluster transitioning laterally to PsiV.
3. Occasionally Delta V - Beta U at the border transition of Beta U and Delta V.