Our floor installation began a couple weeks ago. $10k worth of large 8x48" Wood look porcelain for around 2200sq ft.

After day 1 or 2, we visited the house and noticed issues with lippage, uneven grout lines and feeling minor undulations throughout the floor. We met up the next morning with our contractor, who had brought in reinforcements to fix the issues. The new guys also recommended they start using the big wedge tile spacers instead of the tiny rubber spacers they had been using.

They continue the floor for the next few days, but upon later re-inspection we're still noticing the same issues in addition to duplicate tiles placed adjacent. After seeing it throughout the house in more rooms, it dawned on us that the stagger was also wrong. We had requested the tile be laid out in thirds -- the box also states that the recommended stagger is 33% or 1/3. I didn't notice it initially, but they botched the layout and went with 1/8ths staggered (6" cuts) vs 1/3rds (16" cuts). I feel this makes the floor look more choppy and creates this diagonal pattern that I'm not a fan of. My contractor said they didn't measure the entire length of the tile to get the proper offset.

I also discovered that the wrong thinset was used from the beginning. The bags state "for tiles <15", which got me researching to easily find that you're supposed to use LFT "Large Format Tile" mortar to support the weight of the tile, avoid the thinset pulling on the tile underneath, and most of all to create an even surface and avoid lippage. I'm not sure how I was the one to catch the issue when there was the same label on 50+ bags. The lack of use of proper LFT Mortar is what I believe to be the cause for the majority of issues. He said they really caked on the regular thinset underneath beyond the recommended amount to ensure max coverage, and doesn't feel its as big of a deal as I do.

To make matters worse, there was no leveling of our subfloor -- it wasn't even brought to my attention that it needed to be done.

Contrary to how it might sound, I really like my contractor - I can tell he cares about our happiness and he has already guaranteed that he will fix any lippage issues. But, I can't help but feel extremely frustrated that the labor on $10k in flooring material wasn't done properly. It's such a huge portion of our remodel and and a very important part of it to get right. We told him that if we had unlimited money, we'd rip it all out and have it redone. We're currently on a temporary hold as he was asking for more money for the job (I've paid half), but I've told him that I need to inspect the entire floor including the living room that has piles of our stuff that didn't make it to storage. We have about 4 other contracts with him (plumber, cabinets & 2 bathrooms) that are half paid as well but not fully underway.

I'm just not sure how to continue and I want to be sure my expectations are reasonable. The floors are already covering everything but our master bath and I don't know what recourse I have here. The guy is BBB accredited & bonded/licensed/insured -- Do I have any options?