Problem & steps to reproduce:

Save game. Manual or auto.

Freighter: 500 stack
Pick up, reduce - drops stuff back in freighter
Move reduced stack of 300 to inventory (250 / stack max)
300 gets divided into 250 + 50 (still stuck on cursor)
Place these 50 in other slot, too

Freighter slot that's supposed to hold 200 is EMPTY
Reload game. =D

Happened to me with ionized cobalt. Well...
Is this known yet...?

I got it all on video, too.