I had this issue in beta 1 as well. When playing 2v2 co-op vs AI, some weapons get replaced by a "01_01 Doesn't Exist" weapon (that obviously is useless in battle). In my limited testing it seems to only affect the player who isn't the host, but my friend and I have both experienced the bug. Necron ships end up with no weapons; some other factions (like Tau) lose some but not all weapons.

https://steamuserimages-a.akamaihd.net/ugc/952975870959080324/E9FDD659B1512B9F30B6A8E2D3A68F46FC15C32C/