Currently it's possible to silently use a loop pass that does not preserve MemorySSA in a loop-mssa pass manager, as we don't statically know which loop passes preserve MemorySSA (as was the case with the legacy pass manager).
However, we can at least add a check after the fact that if MemorySSA is used, then it should also have been preserved. Hopefully this will reduce confusion as seen in https://bugs.llvm.org/show_bug.cgi?id=51020.