I had this issue and after discussion with GC and tile co., it was all ripped up and reinstalled. If you are uncomfortable now, just wait a few months until buyers remorse hits. Also, if you were to sell the house, potential buyers would notice. Walk on it barefoot and then ask yourself if you are willing to put up with it forever. If possible, get it done right. Jerilyn, it's very unlikely it's defective material. This type of tile needs to be installed like marble, so they tell me and I went to the distributer to meet with the manager over this issue. She explained the whole thing to me. She was well aware I changed my mind on another bigger project using the very large planks. Not every tile setter can do marble but since this plank is in style right now, they all are trying to keep up. She said they offer classes to the companies who buy their supplies there but no one comes. They all think they know....sigh. After going through the process, I can't see where or how, removing a few tiles and reinstalling is an option. But I am not there. There are 4 points where adjoining tiles are going to meet up. If you adjust one, what happens on the adjoining edges. I am not a tile setter. I guess with enough experience they can make magic. This sounds like a quick fix and then what happens in a month or 6 months? Is this work guaranteed? But if you do this, before you tell anyone its okay, wait until it's dry and you can walk all over it. I saw on TV show they used a hockey puck to slide across the floor. If it's not even, the puck will bounce (lippage). Now, that might just be TV but you need to be double darn sure the job is what you want. In the end, even with a total rip up and the floor was floated to be sure it was level, I still have a few places where there is a tiny bit of lippage. It's not bad or in the walking path and I can tolerate it. The first install was like walking on very sharp edges and would even catch the sole of my shoe. When I ordered new window treatments, the woman who came to measure commented on the tile and then told me of her nightmare in a condo. It's all lippage, so much so she has rugs everywhere. It cost her a lot of money and because she didn't know any better, now she has a lot of rugs and a floor that will be a huge issue at resale. Make your stand, ask questions, go talk to the supplier without dissing anyone. Ask the GC if he would call this acceptable in a different job. I know right now it's about the cost of correcting it and ripping it out and starting over would be awfully hard for him to swallow. Did the GC sub out the tile work because that can get testy? But in the end, it's the GC who needs to work with you, you did hire him, right? I am sorry you have to go through this and I wish you all the best.

Quality? Its on par with builder grade lowest denominator sub contracted tile installation work. Theres also Custom professional master tile installation crews out there. "But builder said the other subs they use would grout and then cover with clear caulk. " As CTEC stated builder is wrong and you dont want his other sub either. What you want is a detailed scope in your next tile contract refrencing industry standards to be met and followed as well as details of layout expected only then will you have written documentation to debate upon.

The contractor is largely correct. The chips might need to be filled depending on what kind of floor is going back down.

Thank you @millworkman and @Kristin Petro for your responses. Here are some photos. I tried to capture the issues but it's less obvious in photos than looking in person. This piece of cut tile is not the same width along the niche, and the cut itself is also not straight or smooth. The tiles are not flush. I know there is a bit of buckling on all tiles, but most of the pieces do not have this issue so I am pretty sure this could have been avoided The contractor said that he is not able to make the cuts so they are the same height across the top (he kept blaming the uneven ceiling and the shadow from the mud, etc., but I am just looking across the tile tops). Maybe the caulk will fix this, but I won't know till it's done. I am rather skeptical he is saying it's "impossible" to line up the tiles. It may be difficult or unnecessary, but to say it is not possible for someone who's done this for 10 years seems a bit unreal.