This has always been the case even in warband if you do it properly? I have done this with bolts many times, one person takes a shield and gives it to the cav while the other xbow takes strong bolts and gives them to the other xbow. The only difference with warband is that it is actually harder in warband as you need a full inventory to do this.
You can see that this is intended behaviour by looking at archers, you can fill your stronger arrows with weaker arrows you find on the ground.
I prefer the system of Warband as that actually feels a bit more polished, only if you have a full inventory you fill-up the stack of whatever you have if your inventory is not full you just take it on as an extra item.
Fixing this would be a royal pain in the ass because that would mean that picking up javelins becomes really ****ing annoying.
For example, if you have a spear, shield, sword and 1 light javelin this means that you cannot pick up a random javelin that is not a light javelin as it won't merge into your stack.
It has always been like this in M&B games, Bannerlord just has an even more lenient approach to it. Also, I'm fairly sure that this is in the base game so don't know if they can even fix it in MP without fixing it in SP which might not be desired.