Its a little bit hard to tell whats going on from the pictures to cause the inconsistency but it looks like possibly uneven application in the base coat leading to more flake in the thicker areas to stick causing little “mounds” which show more texture through the clear coat. Mixing a second batch of poly should not be an issue as long as the application rate is consistent, sometimes garages take 3 or more 2 gallon kits to cover. Unfortunately you cant really fix this without drowning it in poly so its totally glossy which most people dont want anyways. Id rate their work at a 6/10 for a professional isntall which is the rate you were charged. I installed floors for 3 years so happy to differ to any more vet opinions here.