How should I bring up contract violations or deviations to my contractor?

I hired a family owned company to repair a leak and renovate the shower. They presented me with a contract, i.e. the list of things they were going to do to complete the job. I signed it.

Well, today, I noticed they didn't do stuff they said they were going to do in the contract. Example, replacing damaged wood studs with new lumber and installing HardieBacker on all the shower walls.

The work is not done, but I can clearly see they did not replace the damaged studs and just drilled in the drywall over it, plus they only installed HardieBacker on one of the walls.

I certainly don't want to pay for something they're not doing. I'd rather them do the job right or not charge me for things that are not needed. Either way, these deviations are not being brought up to me.

What should I do?