after more testing I guess it is by design (to be more realistic)
The new system of removing items from its inventory slot when in your hands is a nightmare.
say you have a pistol taking 4 slots in your bag and you have it on a hotbar slot. lets say slot1. and you have an axe to deal with Z's on slot 2.
As a precaution when entering a town you take the pistol in your hands and proceed to loot the town.
if you find a soda and pick it up using default action without going into your inventory it may place that soda into one of the 4 slots for your pistol even if you have a pocket empty on your jacket.
you go outside and there is a zombie so you try and change to your axe on slot2 but you can't because the pistol now has no free 4 slots to go into.
by the time you sort it out you could be dead.
(perhaps the ability to pin an item to the slots it's in or an auto manager that moves that pesky can into a free single slot to make room for the 4 slot gun)
when putting stuff in a real bag you are not tied to specific square slots, if it fits in the bag with other stuff it fits, regardless of its shape, other stuff should move around to accommodate.