Just came back from watching, and this is the exact thing I was thinking of. EVEN IF David was able to hack into the system in the downtime after McBride's character stated he shut things off, that still seems hella convenient. IIRC David had command codes in Prometheus, and being a 'son' of Weyland might give him hardwired codes, but the quoted is still a huge, huge oversight.
Also, if David is somehow (presumably) still out there (after having murdered the rest of the crew and the colonists on his random star travels in an attempt to eliminate all organic life), how has Weyland-Yutani never encountered him by the time Ripley and the Nostromo land on LV-426 or w/e.
Not a big fan of Shaw somehow getting off-screen fridged by David either, tbh.
Or why Captain Orrim or w/e would suddenly pull a "I'm stupid" and believe David, follow him down into the alien nest, and then look over the damn opening egg.
Basically everything from one of those '10 things that make Alien:Covenant Stupid' lists is a giant issue.