The rebar most likely was holding up the form board and should have been removed before the concrete set.

The plumbing should have been encapsulated within the pool shot.

I'll take a guess it was a hot day when the pool was shot. Cracks are developing because the concrete is drying too quickly.

Document everything with photos and any contacts you had with your builder abut any of these issues.

I did. They’re saying it’s fine and that the plumbing will get covered in tile. Is that ok or does it need to be redone?

Gunite cracks

I hear too often by contractors, that imperfections can be fixed with either tile or coping.

The outside of the spa, if I'm correct, will be exposed and therefore have tile applied? If so, the forms should have been stripped during the shot and the gunite crew would go around the perimeter and make it true. That way tile or any other material can be applied to an even surface.

The cracks are most likely shrinkage cracks from the heat. The shell should have wet down after the shot, but not super soaked, to prevent this. Going forward, within 24 hrs, the shell should now soaked daily, multiple times to allow that mass of concrete to cure properly.

Water is needed as part of the curing process especially in that Texas heat.

Sometimes we set up an sprinkler and keep it wet all day. Some have set up soaker hoses around the perimeter.

The concrete takes 28 days to fully cure and it generates it's own heat. Drying too fast is not good without the aid of water.

I notice water collected in the deep end. Is there a groundwater issue?

It had been watered per the schedule, 3 times per day starting the day after gunite

Water in the deep end has accumulated from water the gunite and rain