If you solve the problem by saying "she was given all of these random items by creatures beyond human understanding", it raises basic questions like "Why would they do that?" and "How did they do that?", and a spin-off question from the first, "Why did they choose to give her these specific items?"

On the other hand, since most of these sound like things that could just be found in a badfic or swiped by an Agent while their partner wasn't looking, it would make more sense to have your agent pick some of them up from HQ.

Let's run down the list here:
Fudge/Cocoa mix: you would've probably eaten these already, and neither is really something somebody would want to keep in their RC for very long anyway, for fear of the minis eating it. Irrelevant.

Bubble pipe: This seems like some sort of whimsical item that an Agent would've picked up at some point and eventually gotten bored with. I can see this being traded away to your Agent for pretty much anything, picked up at the General Store, or perhaps it was just left in the RC by whoever was using it last, if you're going to characterize your RC as previously occupied. Same for the the urple yarn, the snowglobe, and the non-Infinite notepad. Highly plausible.

Minis: there are several different Mini Adoption Centers scattered around HQ, and new Agents usually tend to go out and adopt a mini or two that matches a preferred fandom. Highly plausible.

Classical Music: I'm not sure how music itself would be physically present, but it would be reasonably plausible for the song to be alongside other assorted classical music on a CD from Small Murphy's shop.

Wilver knife: This sounds like something that an Agent would've picked up on a mission and traded in to the Armory. Z would probably be happy to get rid of it for a reasonable price, since wilver tends to make people's eyes water when they look at it. Reasonably plausible.

Hypospray: The Supply Depot actually stocks a few of these, in case they'd be needed as emergency items. Highly plausible.

Urple Infinite Notebook: Also something that an Agent might have picked up on a mission. This sounds like it might potentially occur naturally through confusing phrasing. Reasonably plausible.

All of those could just be summarized with a few sentences that essentially summarize to "(Agent's name) had been travelling around HQ all day, collecting a myriad assortment of items of varying levels of value. Also, she adopted some minis.(minis immediately commence causing trouble)".

The concrete mix is a little less plausible, but if you really want to include it, it could be glossed over by something like the Agent's partner looking in the bag and says "Is that concrete mix in here? Where did you even get that? (exasperated sigh) If this spills on the floor, you're cleaning it up.". It would be more of a one-shot joke than something that would be likely kept around, though, because it would harden into a misshapen blob over time and not really be useful for anything after that. I guess it could be used to throw at something, maybe.

Anyway, that covers the gifts within the realms of reasonable plausibility, but the Cybermat is significantly less plausible, and would probably need to be explained by events that occur in-story. Maybe it could have wandered in through a plot hole with a small clutch of other modified Cybermats. The DMFF could be sent to go clean them up, but one would escape, wandering into the path of (Agent's name), who names it and brings it back to the RC with her. Eventually it's found, but after (Agent's name) petitions to keep it, the Cybermat is allowed to stay on the condition that it stays in the RC and doesn't try to cyber-convert anything. It's not as though a Cybermat is the strangest pet an Agent's kept.

Speaking of Cybermats, here's Tooth back. His outer shell should be significantly harder to damage now, since it's been enhanced with tironium, the same stuff the Decepticons make bladed weapons out of. There's a surprisingly large amount of it in the sub-basements. At some point I should probably investigate where all of this extra-dimensional technology came from, since some of it seems a little too convenient to have just fallen in through random plot holes.

The ending of Sherlock series 2 has made there be much bad angst.
And good angst, actually.

Could my agent know of the PPC from the real world?