If you are in the spidertron and you are on a location where a hex core can appear, then if the hex core does spawn there the spidertron will be voided and you will appear next to the hex core. I'm not sure what happens if the character is on the location. (I'm not 100% sure on the events from the one time it happened.) The time it happened to me was when I was using bots in the rare spidertron to loot the dungeon chests. When the last chest was looted the hex core spawned and voided the spidertron. I just restored an autosave to get it back.

Sorry that happened. It's another edge case I haven't checked for. Newly spawning hex cores check for anything in the way to make sure that nothing is clipping after they spawn. I forgot about the possibility of a spidertron or any other vehicle (modded included) hovering over the spot. Come to think of it, this can even kill robots flying over the area. It's more about trees, rocks, and biter bases clipping the area, but I suppose it should additionally filter out anything that can hover or "stand over" other things, since it already filters out players so as to not accidentally kill players in mech armor.