Seems the collectable stats not tracking properly is an acknowledged glitch with the game (one that's never been fixed). I went through with a guide on my collectable cleanup run so I know I was getting everything, but one of the later levels continued to show that I was missing something (even though I definitely wasn't). Judging by what I read online, it's reasonably common.
Apparently the only reliable way to safeguard against it (on the PS4, at least) is to set the system to keep games running when you turn off so that you can just keep it paused, and simply resume playing when you turn back on. That way you can get everything in a single "session" without the game ever shutting down or even returning to the main menu, and apparently that should ensure it tracks properly.
Simple enough to do, but you have to delete everything and start again from scratch to do it and it kinda killed my enthusiasm back when I was originally playing.
Kinda like that f*cking bug in
Mad Max where the stats would discretely fail to record one random scavenging location when you cleaned it out... and there were almost 200 of them in the game. If it happened you had to start all over from the beginning, and unless you knew about it beforehand (I didn't) you wouldn't notice until you ground your ass through to the lot only for the trophy to fail to pop. Almost broke a controller that day
EDIT: Have I mentioned that before? Just got weird déjà vu.
