I finally got around to testing a double sniper rifle build using a rare Needler and a rare crafted Longlas. Before I  used this particular combo the game was running well. Smoother, slightly better FPS etc. Once I equipped this combo of weapons I started crashing mid mission, crashing after clicking on the star map and the other known bug of being unable to collect loot after the mission (if I managed to finish one, this happened only once). Went back to a different combo of sniper rifles and haven't had a single issue since.