A non-anthro feline Sue? That's... certainly unusual. Given that the side effects of cow milk in felines involves loose stool, I've also got to congratulate you for avoiding a very ugly pun. I've also got to congratulate you for getting a curiosity joke in fairly subtly.

Some nitpicks:

• "A portal opened and through it two agents entered the abandoned warehouse." is probably a compound enough sentence to require a comma between "opened" and "and". There are two separate verbs (opened and entered) and two separate subjects (portal and two agents), so there are two independent clauses without a subordinating conjunction but with a coordinating conjunction. While it's not a perfect rule of thumb, if you can replace the "and" with a period and still have working sentences, the "and" needs a comma. To quote JulyRose : "An independent clause can be a simple sentence by itself; a dependent clause would be a sentence fragment by itself."
• It's not clear what "Well, abandoned." is stating. Could a word like "mostly" be necessary?
• "Its current owners saw no particular use for it so the A-Team were squatting the building." needs a comma between "it" and "so".
• "The van was parked in the middle of the spacious room and in one corner some living/sleeping space had been set up." takes a comma between "room" and "and".
• "ball-point pen" has been largely standardized to "ballpoint pen".
• "If Mrs. Baracus had called the phone in the van BA would have heard it ringing too." needs something separating the adverb clause from the independent clause. The easiest solution would be a comma between "van" and "BA".
• Formatted as "Stupid Sue not even", Stupid Sue is being a noun but doesn't really have a verb to operate with. You can add "is" after it to get the sentence flowing smoother, or a comma after it to set it apart as an interjection or address (in which case you're using a silent but understood subject for the reset of the sentence). If you're intending slightly broken speech, neither of these changes is necessary, though.
• "It was all alone and Face took pity on the little creature." takes a comma after "alone".
• "Perhaps her foreign correspondency ended,"... I'm not quite sure what word you wanted here, "time as a foreign correspondent" perhaps? Correspondency seems non-standard.
• "The big guy is kind to all animals. Except imaginary ones," Tasmin added." may demonstrate a pause better by putting the "Tasmin added" in the middle and/or modifying it to something longer, such as "Tasmin paused for a moment, before adding". If it's an obvious enough addition that any pause in her statements would be very short, this isn't worthwhile, but it can add a bit of variety.
• "In fics where Face has nightmares Hannibal usually treats Face like a little kid." could use a comma between "nightmares" and "Hannibal".
• This is probably a joke or colloquialism I'm just not getting, but "attachment is no place for a fugitive." seems confusing, since attachment isn't a place in the first place. Moving to "a fugitive has no place for attachments." is clearer and moves to active voice.
• "That has too much lactose and kittens are often lactose intolerant." could use a comma between "lactose" and "and".
• "Everyone went to their assigned rooms and the agents joined Murdock and Face." could use a comma between "rooms" and "and".
• "Now Face has something to cuddle and he can let all his childhood suffering and angst go." might want use a comma between "cuddle" and "and". This is spoken word, so you can get away with missing the comma if the phrase needs to feel like it was blurted out, but I don't know if that's the case.
• "When Face was done talking he pulled the covers over his head and Amy and Murdock knew it would be a long time before he would talk about his childhood again.", on the other hand, really needs some punctuation after "his head". Minimum for correctness would be a comma, but it might be worthwhile to switch out the "and" for a period; multiple "and"s tend to grab focus and increase pace at the cost of clarity, and you're getting a bad deal here.
• "The friend, Toby, had had his arm broken by some local crooks running a protection racket. Because of this he could now not work." The "now" is probably superfluous, or at least unclear. That could go to "could not work" or "could no longer work". On the more nitpicky side, "had had" is technically correct, but ugly and passive. "The friend, Toby, explained that some local crooks running a protection racket had broken his arm." seems stronger to me.
• "When Face and the rat got to the car, Face popped the hood and Hannibal jumped up from the engine space (the engine had been taken out) and aimed an assault rifle at the rat." is a hilarious mental image. Could also use a comma between "hood" and "and Hannibal", or even replace the "and" with a period to reduce overall sentence complexity -- although at the cost of slower pacing.
• "The agents were looking at the proceedings of the scene from a safe distance. Relatively safe in an environment that only had a permanent-looking structure because Allison imagined there should be a building." There's no independent clause in the in the second sentence. I'm not sure if that was intentional or not; there are some uses for such things. If not, it'd probably be safer with a comma replacing the period after "distance".
• You probably want to specify who Sammy is before having someone inform him of anything, nevermind put out a cigar on him. The place where Toby gives directions might be a better place to name-drop him.
• "Hannibal loves playing the characters that set up these shops and he loves his cage getting rattled." actually works pretty well as-is, but it's not benefiting much from the lack of a comma between "shops" and "and", even if it doesn't hurt as much as other examples, either.
• "gave the kitten to Amy who he hoped would be more responsible." would use a comma between "Amy" and "who", since it's a nonrestrictive modifier.
• "With the rats disposed off" should be "of".
• "'causing all of them to behave" probably doesn't need the apostrophe, unless it's a shortening of a longer word.

That Sue was ... insidious.

[Tasmin nodded. "Make a note of that."
"I will. As soon as you stop sitting on my pen."]

This made me snort.

Nice mission!