It was on a heist mission to get the prism, taking a detour and causing a highly visible ruckus that by all rights should be talked about up and down the sword coast seems like a super dumb idea.
Unless this WAS the heist mission.
If the Prism Heist was occuring in Baldur's Gate, then swooping in and taking it before the Gith get their hands on it would be considered worthwhile, despite the problems it that its noteriety would cause.
It also doesn't make sense why they'd have untadpoled prisoners on the ship either.
It grabbed them during the attack. You literally see it in the cinematic, the tentacles slap bunches of people and they get poofed into the pods.
Thus, it's highly likely that this is where the Origins/Tav get picked up. Them being random bystanders who simply happened to get grabbed during the attack (With of course Karlach/Wyll coming from the brief jaunt in Avernus)
As for why grabbing random people?
It could be a way to mask the real reason for the attack. If you make it seem like just a random abduction attack then you don't raise the suspicions of the Gith about the fact that you were directly targeting the Prism Heist (Which seemed to have worked because the Gith had no idea that the crashed Nautiloid contained the Prism and that survivors of the crash would carry it directly to them)
