"...failed waterproofing since the contractor didn't follow the plans and didn't waterproof. "

I think you answered your own question

Your house will rot from the inside out if this isn't addressed soon. You need to get your contractor's attention immediately.

We brought this all to their attention. They're refusing to fix the house and refusing to give our money back.

Exterior pics?

Looks like you have concrete walls. Water may be coming in through concrete and therefore you need a mason to address that. It has nothing to do with the window installation.

Could also be the roof.

Post some outside pics.

Here are some photos - inside and out.

We have CMU walls. He did not waterproof them. As for the windows, he didn't install a buck (removed the original) and didn't install flashing. Mortar and brick is in direct contact with the frames. He disregarded the local Building code as well as our approved plans. He is the permit holder for the job.

The issue could still be the brick. Water will go through any openings in the brick regardless of whether he used flashing. He seems to have installed replacement which is most common.

Not saying 100% thats the issue but whenever I see ubiquitous water leakage and there is brick, its usually a masonary issue amd not a window installation issue.

Lastly, did the window contractor create new openings?

This was a complete facade renovation that the contractor went rogue on.

Blue skin on CMU was supposed to be installed - he didn't do that.

Foundation was supposed to be waterproofed - didn't do that (small section)

The windows were supposed to be installed in a buck that was fastened to the masonry wall and flashed - that didn't occur.

The rough opening was large. The new windows were smaller than the previous ones, which were in a buck and flashed properly.

Here are some photos. You can see that there was enough room on both. Both windows were smaller than what was previously there.

No easy fix there. Sadly.

Thats different, i feel bad for you. Did he give any sort of explanation as to why they deviated from what was clearly stated in your contract?

What did the contract state in writting? Anything verbal is meaningless.

No explanation whatsoever. He also substituted the brick ties with those that are not code compliant. He just went rogue.