Hi,
I'm not sure is this is a bug or just something that could be improved, but when using the alternate inventory system, if you have more weapons in the craft than ammunition, they will steal ammunition from soldiers inventory at the start of the missions.
I have attached a save file to demonstrate the issue. The craft has 1 soldier with 1 rifle and 2 clips (+1 in the rifle) and 3 empty rifles. If you send it to mission, the 2 clips in its pocket will be moved to the rifles on the ground.
It also happen in the inventory screen at the base if you don't have enough ammunition in stock.
Ammunition that are inside an equiped weapon are not affected.
To be fair, this is exactly how to original inventory system is also working, but the original system has always been a mess.
The new system is great, but I've had a few bad suprised because of this issue.