The only bit I found egregiously dumb in Covenant was Oram leering over the egg just because David told him to, when only moments before David had shown he was less than sane of mind and probably had ulterior motives. To then have Oram decide, "Yeah, nah, you're probably trustworthy," came off as totally illogical.
Other things people regularly pick on, like Faris losing her shit on the lander, seemed pretty fair to me given what was going on at the time.
Prometheus was much worse in the dumbness stakes imo.