Some of the grout line widths would be taken care of by the grout, but the pattern is obviously misaligned with black dots out of sequence and alignment. I don't think it is unreasonable to expect the pattern to be laid properly. I would expect this to be redone.

Thankfully it's not yet grouted. To repair the pattern and some of the spacing issues, individual tiles can be popped off and reset as needed. It's better to address this sooner rather than later. Obviously before grouting. But also the longer it sits, the stronger the bond.

If it's a small area, there you go. If it's over a larger expanse of floor, then woof.

Poor sheet alignment, yup, it can be the sheets themselves that are deformed/compressed, or the installer just setting the sheets poorly. Either way it's an installer issue. An installer can halt an installation at any time versus choosing to install a deformed product. An installer who thinsets down bad tile is accepting responsibility for the defective tile as well as the defective installation. It's called worksmanship. If it's not too bad throughout, a grout matching the light colored hex can aid in disguising sheet alignment issues. As can a throw rug.

Then there's always the issue that some installations really can't be rescued. In capable hands, a rotary hammer with a wide spade bit, held at a low angle, will shear those hexes right off the thinset. If it's electric radiant it can still be done. A squawk box or continuity alarm can be used to indicate if the RFH cable is damaged during and demo and/or repair.

Not easy, not fun.

The installer saved 20 minutes of labor during installation only to add 20 hours of labor for remediation.

Choices.

Is this by any chance Merola hex? We did a bathroom with their tile last year (or at least tried to!) The sheets were a mess and our tiler spent hours pulling tiles and trying to realign them (and even after all that I still notice spots here and there where the spacing isn't quite right). Fortunately ours was all white so the pattern piece wasn't an issue, but the sheets have to be matched carefully to avoid those issues, and it would not surprise me if the pattern on some of the sheets was off to start with. We gave up and switched to a more expensive tile with far fewer spacing issues for the shower floor--wish we'd just done that from the start.

And yes, they'll need to pop off individual tiles to fix it. A pain but worth it since this will bug you forever to look at.

I think it is Merola. :(

Or maybe a different brand but the same factory.

Metro is the same tile with different branding (and I'm sure they sell under other brands too). We did get samples of it and it looked okay based on that, but the actual tile was sloppily meshed and constantly chipped during install--if they're already pulling some tiles, check for any that have chipped edges too. And I do think some of this is just your installers not being careful about aligning the sheets, which could happen with any tile. (In your second photo, you can clearly see the edge of the new sheet.) Either way, on them to fix. So sorry you're dealing with this!