Let's say you are collecting treasure from more than one sea monster or enemy ship after an exploration voyage; let's further stipulate that you have one empty bin in your materials storage (silo). And further, let's say your stockpiles of gunpowder and silver are both maxed (i.e., the next single piece of gunpowder or silver that you attempt to collect would cause your last silo bin to be occupied. Now, in collecting from two sea monsters in succession (without bothering to return to manage your materials inventory in between), you find and collect 1 silver from the first monster, and 1 gunpowder from the second monster/ship. Upon uncovering the gunpowder, the game does not realize that there is no place to store it (the numeral is not drawn in red), and the gunpowder is lost.
It would appear so, have heard this before from others. I know that if you receive grog in chest, it will flag a warning before you 'collect' if all your stores are full and you have nowhere to put it. You can then leave it there until you have room.
It should probably get changed so that you can choose to cancel collection of the material to make room, like you can with chests, with the option to throw out the material if you didn't want it anyways and just want to set sail again. Give us two buttons: [Return] [Discard], and on returning, it allows you to go make room. Right now, just be careful on collecting if you don't have storage space!