OK i got savegame for you, UFO#40 - Harvester, heading towards base in africa, if you compress time (1h compression) will get there in 2 seconds, base has 2 antimatter storage buildings, has 12 soldiers equiped, has 2 stiletos, 40 workers. mostly empty otherwise, used to dissasemble UFOs.
Same crash happen's, same conditions, once you remove antimatter storage from base (tanks are empty aswell) crash never happens. Just to make sure you read it carefully:
Linux, Ubuntu 17.10, official game release 2.5, no mods and/or patches.
would be nice to tell me if you managed to reproduce the problem, or it happens only in my setup.