The square-ish apots were all in the same general area.

I would have said those were sweat drops but not sure. The last one is a lap mark where too much got applied.

Some type of chemical reaction to a contaminant. The final coat reacting to whatever got on it - photo 1 and 2.

Photo 3 and 4 are roller marks. Roller got thin in that area. Poor coverage.

Photo 5 is a lap mark as Hallet suggested. The edge looks thinner than the field.

Would the contaminant have most likely bee on the floor before the final coat or is it something that fell during or shortly afterward? This is Bona Traffic HD.

Contaminate would be prior to final coat.

It does look like a sweat mark. How warm is it over there?

It was done in January, ao not very warm inside. The contracted installer is trying to blame us for the marks, but we weren't even in the house. Trying to understand the timeline becauee we're all meeting with the company owner (who contracts out to the installer) to hash this out. If a contaminant had been there before the prep screening/sanding, I'm thinking it would've been removed. This would've had to happen after the prep and before the final coat?

You said a few years ago in your post when was it done? What were the issues before the refinish?

We had a water spill upstairs in late 2021 that required removal of a small amount of flooring downstairs. The whole house was refinished - upstairs snd down. The blemishes in the pictures in this post were the only problems. The installer applied a 3rd coat 4 days later and that coat never hardened. They came back and did a total refinish - sand and recoat - but left widespread sanding issues that they don't want to take responsibility for. Very long, unpleasant experience for us :/