There's definitely something odd going on, but tbh I think a lot of it can be attributed to the extreme situation at hand rather than anything shady the fireteam themselves are doing. Both Chalco and Fenchurch are longstanding members of the Hidden who are often trusted with high security work.
Tbh, I read the repetition of the "we are the only extant fireteam" line to be for the dramatic effect of not outright saying anyone has died. Clearly another team/other teams of Hidden agents have come down here, but it is so dangerous that none have survived and/or returned. Because Chalco is there leading the expedition, I assume that means Ikora thought no one else could be trusted on counts of both security and survivability.
Chalco Yong is an important member of the Hidden (and near sole confidante of Ikora) who has been involved in investigating major plot developments of the past few years. She helped track down Mithrax before Season of the Splicer (listed here under her hidden codename CHA-319), kept tabs on Crow just after he was risen from Uldren's grave, and while the Martian Missives lorebook should be taken with a shaker of salt, she's also mentioned to have been investigating Fynch during TWQ as well. I read Chalco's reluctance to answer Fenchurch's question directly as more likely regret and/or fear of having lost other teams or team members on this extremely fraught mission, and steeling herself to get the job done without freaking out like Fenchurch is doing.
Honestly, as for the Fenchurch Pineapple Incident, I think that was supposed to be a comedic in-joke for people who remember the running gag of Eris' shock at the existence of pineapples from Arrivals in The Singular Exegete lorebook. Yes, she was concerned about the pineapples being poisoned since they came from a Guardian with unknown loyalties seeking knowledge of the Darkness, and at that point Eris was worried about interference from Savathûn. But to my knowledge we have never received any further information about the Guardian Enina, and have no evidence that there was actually anything wrong with the pineapples at all, just Eris' suspicions. And I don't think any of this has any connection to Fenchurch. Fenchurch is known for finding oddities in his exploring (as Tess will repeatedly tell you if you idle within 100m of the Eververse shop and breathe) and if anything, I'd suspect Enina would have gone to the curio collector and gotten the seeds from him rather than the other way around. I think Eris' extreme reaction to Fenchurch's food is because of the fact that 1. Fenchurch was casually eating the exact pineapple fried rice dish that Eris was trying So Hard to make but couldn't because pineapples have been almost entirely forgotten in post-Collapse civilization (what the hell, man), and 2. bad memories of that uncertainty with Enina. Also, 3. it's hilarious.
As for Lisbon-13, he's the one with the wildest story out of the fireteam, though here he acts the most normal out of the three Hidden members visiting Oryx and really doesn't seem to be doing anything suspicious at all. He's the sole surviving member of the Kentarch 3 fireteam, as you mentioned. I'm honestly kind of baffled at the fact that he's allowed to do Hidden work now, but I guess he seems to have worked it out with Ikora? But yeah, his fireteam attempted to infiltrate the Black Garden to acquire the Divinity exotic. While it is extremely unclear just what happened (as there are multiple conflicting narratives and possible doppelgangers and other weird stuff at play, thanks Garden) it's clear that he killed the two other members of his fireteam after they started behaving extremely strangely and all of them were hearing duplicated voices, possibly corrupted. Lisbon is in such pain after killing them (including the one who was his lover) that he literally asks his Darkness doppelganger to erase his memories of them - and they do. I legitimately thought he died after this, but we found out that he is not only still alive, but was able to recall lost memories of his fireteam using Savathûn's Altar of Memory. How he got from there to joining (or re-joining) the Hidden, I have no idea.
Anyway. Definite weird stuff happening, but personally I'm way more inclined to chalk it up to the sheer freakishness of this whole Oryx's corpse situation and the intense consciousness-related Darkness powers surrounding it, rather than to anything suspicious the fireteam themselves are doing here. I really hope we learn more about what the hell is going on down there on the ocean floor. Also I really hope Lisbon is okay, that guy's been Through It.
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