Using: Mekanism-1.11.2-9.3.1.305
Breakin doors, and slabs crashes the server when mined on vein mode, probably all modes.

Do you have a crashlog? Please upload it to gist.github.com and place a link here.
Also please update to 9.3.1.307, there've been a couple fixes to the Atomic Disassembler, but I think they're already in version 305. Nevertheless, an update would fix a lot of issues.

Just ran some tests, can't reproduce this on any mode with any kind of non-solid block. Interaction issue perhaps.