I replaced the starting autogun with a master-crafted Boltgun from the store (not crafted), and in-mission it disappeared. At first I thought it was an animation bug, but on mission exit found that the weapon had been removed from my inventory entirely on launch--subsequently causing the animation bug.

Secondary concern: enemies and enemy emplacements ignore terrain for line of sight/attacking; this is absolute hell for the clomping Crusader, and has caused me to die repeatedly without being able to even attempt to engage the enemy. Not ignoring cover, but terrain itself. Huge hill that I have to navigate around before I can even highlight a mob? Autogun spam and rockets chip my health to zero. Giant rocks/walls between myself and a turret emplacement? Get shredded through the walls before I can even see what killed me, respawn, and get close enough to see that it's an autocannon turret before again dying.

It can be partially circumvented as the Assassin, by dodging to and fro and using up all of your adrenaline, but it's a pretty glaring bug for the solo player who favors heavy weapons.