Confirmed - good find!
It looks like the game lets you merge stacks of items with different properties but the same name, resulting in a single stack of all one kind or the other. It works both ways - whichever kind you're adding to is the one that stays. To replicate you'll need a stack of at least two thrown weapons, alchemy of at least 5, and the ingredients for a weapon imbue - ectoplasm/sulfur, ectoplasm/ash, and black-spotted shroom/noximander venom all work at alchemy level 5.
- Imbue a single weapon from the stack
- Put the imbued weapon in a spot in your inventory
- Pick up the rest of the stack of non-imbued items
- Drop them on the imbued weapon
I guess this isn't a big surprise given that the game typically only checks item name in many situations. The obvious fix would be to verify that all the properties of two stacks of items match before combining them, but I don't know how much of a pain that would be to code. A more subtle fix might simply be to change the name of imbued thrown weapons, the same way as is done for melee weapons and bows. Unless the names are distinctive between +1/+2/+3 of each kind of imbuing and all combinations, though, it would still be possible to exploit.
Honestly, though, the thrown weapon specialist deserves a break like this. Aside from the gold farming aspect of the bug, I'm not sure it's worth fixing. It might be nice in Book III simply to allow imbuing whole stacks of thrown weapons with a single set of reagents, unless of course BW has other plans to improve thrown combat.