I think the problem with the ending is just how it affects the film's pacing. I didn't mind the ending the first time I watched it, but when I rewatched the film, that section was a drag to get through. Now, when I put it on, I usually shut the film off after Michelle escapes the bunker.
The problem is that alien fight is just tiring, especially on repeat viewings. It feels almost tacked-on (not story-wise, but pacing-wise. The best comparison I can think of would be if the LOTR movies had adapted the Scouring of the Shire at the end). Her escape from the bunker is a nail-biting sequence that always has my heart racing and puts me on the edge of my seat. It's basically the film's climax.
But then, you're almost immediately launched into another action scene that despite being grander, doesn't really have the same stakes as before, and really feels similar to what you had just seen (it's a really tense scene with Michelle coming close to death several times that ends with her surviving by thinking up a clever solution, like kicking over the acid or breaking the lock). It's why I understand why people say it feels tacked on. The climax of the film: escaping the bunker where almost the whole thing was set is over, and then the main character starts fighting aliens in a scene that also goes on for way too long. I don't think those weird dog things were needed; you could have just had the ship. You're already kind of burnt out from the bunker escape, and you're giving this action scene which just drags on.
Funnily enough, the film is produced by J.J. Abrams, and this is the exact same problem I had with his Mission Impossible 3. After the midpoint of the movie, the film just hops from setpiece to setpiece barely giving the audience any breathing room, to the point where I'm just exhausted before the end of the movie. I'm not blaming J.J. for it happening in 10 Cloverfield Lane, but I think it's a funny coincidence.