Looking for insight

I am a new first time homeowner and have no knowledge of flooring, contractors, or anything house related. I purchased a new construction home and wanted to take out the carpet to have LVP installed to match our downstairs which already came with it. When our flooring contractor started the demo, he said that there was a lot of debris and plaster that had to be cleaned up and said that when the builders were installing the floorboards, the screws were not installed to sit flush with the flooring so there was a bump that he now has to hammer down into the floor so the LVP will lay flat. I brought this up to our builder's site manager and he's saying the way the screws were installed is up to code and standard. Not sure who to believe, I understand there may be a different "standard of work" when carpet is being installed but it's crazy to me that there wasn't any afterthought of "oh what if this owner later decides to install flat flooring". Is our contractor being dramatic or is the builder shifting blame here?