I replicated it with blocks in that exact map location. So I simplified the test further and opened a new baseplate file and put in a 0.8 thickness WedgePart and tried dropping 1x1x1 cubes and this happened every so often:
Seems like the parts were being simulated at 60hz which is prone to tunnelling. We will make some changes to deal with this type of situtation In the meantime, I recommend using Fixed if you are frequently simulating small/thin parts.