No they can't. Take a look in the editor, none of those containers have the Respawn flag checked. Without that enabled, it's impossible for them to respawn. If you think that you're seeing stuff get put into them then it's just a container that you missed before, or an NPC is putting something in them.
Well for one thing, the Raiders in Evergreen Mills don't respawn. A couple do do but most don't. And it only makes sense for them to do so because they've been told to do that. Containers have not been told to, in fact they've been told to not respawn at all. And if what you think you're seeing was a bug, then it would affect all containers, including the so-called "safe" boxes like First Aid Kits. The game won't differentiate between containers, they're all the same to it. So if a bug caused a Dumpster to respawn, then it would affect an Ammo Box as well.
These are areas where NPCs don't(or can't) go. For example, the garbage dumpster
inside
Evergreen Mills. No NPCs venture in there(the Raiders being loooong dead) to place any items.
Here is another example. I am sure we all know the wonderful CTD issue that Fallout 3 likes to do from time to time(a sign of a fun game is that I go back to it time and time again regardless of the crashes), right?;) Well, let's say I am entering Meresti Metro Station. I save the game before entering(I have over 1500 saves at the moment). I enter the Station and the garbage can in the entrance is empty. I go a little further along and attempt to save again. This time, I get the CTD. I will either reboot(if I played for a while) or restart the game. I then reload my last save, which is just outside Meresti Metro Station. I enter the Station again but this time the exact same garbage can that was empty the last time I entered now contains an item or two. It is the exact same timeframe as my previous entrance except that there are items there this time.
I am not arguing with you just for the sake of arguing.
This is what is happening to me, and it looks like to Michael as well. It may be a bug, like you say, as we both know not all of them were squashed in the final official patch. However, medic kits and ammo boxes remain empty forever, so I don't know how it happens.
In the end, it's not a huge deal as it doesn't break our games and make them unplayable. It's just an interesting little mystery.
Merry Christmas!:)