I had some similar to what Andaius said, one of the Dynamite I picked up was equipped by the PG and didn't stack with the normally looted dynamite, and masked all the others. But dropping the PGs one revealled all the others and they had added up correctly.
Yep, I've had the same thing happen a lot when picking up Legion throwing spears, too. I discovered that both dynamite and those spears appear to have two seperate states before you loot them- either 'still in dead mob's inventory', or 'not in dead mob's inventory' (equipped in their hand, or laying on the ground nearby if they dropped it). The ones you loot from their inventory appear normally in your inventory afterwards... but when you pick up one that was either in their hand or laying on the ground, it will then 'overlay' those other items of the same type, in your inventory. So, even if you looted 5 dynamite from a body and 1 dynamite from his hand, you will only see '1 dynamite' in your inventory, afterwards.
So, anytime you go to loot a body, and you see two instances of the same type of item listed, for example:
1 Healing Powder
1 Throwing Spear
3 Throwing Spears
1 Machete
Like so.... the single throwing spear listed, appears separately because it's either equipped in their hand, or lying on the ground nearby- try to avoid taking the single throwing spear/dynamite in the loot list, and you will avoid that problem.