I've tried this in 3 different sectors were I found dropped missiles after ships were destroyed. Tried to remotely collect using both an Elite Vanguard and a Peregrine Sentinel. Even tried it once while standing inside the Peregrine behind the captain while she 'carried out orders' to collect wares. This resulted in her getting stuck and sitting on top of the missiles until I told her to continue on to something else....
It only seems to happen with collecting missiles. I haven't found other 'ammunition' to test this on yet.
Neither ship had missile launchers installed. Not sure if that would cause them not to be able to collect the containers but I feel like it shouldn't....
