Everyone has been suspicious of Ishani the most, also the corrupted db being accessible from her room has also been a huge argument against her, her being an accountant of Synthstar would just make it certain and possibly that would be the clincher for Pandora should she arrive. She is the easy target. Also the scene about her getting angry about the operation of the mech and the moving of stuff in the bay just makes her more suspicious. But you can explain most of her behaviour away as a bureaucrat who likes knowing about things before they happen because her new found position on the Endurance and the task of conserving resources has made her a control freak. And a hacker that hacks the Endurance main system to corrupt it, can probably hack their way in and out of rooms (if on board the Endurance) or just straight up access it remotely (if not on board).
I also think Pandora is quite suspicious. For one, she can hack Paige within Endurance whose systems are down. Who's to say she didn't create this mess and tried to then act like the savior. If she has no idea of echo units and Skylar, then she might have been the one to fudge Ishani's record both times (like even before they were awakened) in order to create a possible scapegoat later on. We haven't exactly established Ishani actually worked/s for Synthstar yet. If someone can hack the Endurance mid-journey to create this mess, they could have also done it pre-flight and also mess with the manifest before they left. Skylar could only know the initial records for each person and notice the discrepancy after the recovery of the db only because she had been one of the first to awaken and had looked at the db early on, that doesn't mean the initial records were not tampered with.
you can easily see a psychology explanation on MC, having been abandoned by his mother, his innate need for female warmth, led him to seek love from all women around him, which eventually led him to being a manwhore as others describe him, but ultimately one that also cares for them. I can also see an explanation about how people like that, who have inclinations towards multiple sex partners initially reject the idea about themselves due to societal norms, try to go monogamous and end up failing miserably and also acting remorseful towards the victim. But they also come to terms with it eventually and instead go full honesty on everyone and into fully polyamorous relationships, embracing who they are and also care fully about all of them, thus satisfying their own needs for love and care. I won't profess that this is all valid science, but we've all seen this kind of reasoning before so it wouldn't surprise me if it's the reasoning here and why Bethany is such an issue for him. And being who he is, he still cares for her and would love to be with her.
