I do not know. And Itch will not tell how the mechanics work exactly.
I remember there being threads where games were positioned too low and it apparantly was a bug, but I do not remember those threads mentioning quarantine.
It's unlikely that your game should be near the bottom with a steady traffic. As far as I know, quarantine should not affect this at all, even while in quarantine. At least not directly. A game ist just not shown as a side effet and there is the warning message. But it would make no sense to directly count the quarantine as a popularity metric. It would also not make sense to "punish" quarantined games. So I think it's a bug.