Just when things seem to be going well...... this!!!!

Holes, defects, etc in the concrete particularly when they are deep, encroach on the concrete cover (the concrete between the reinforcement and the surface of the concrete) and therefore you should repair them, to protect the reinforcement. All standards of practice on concrete (residential or otherwise) say you should repair all surface defects.

In ratter's case for instance there's timber shavings and stuff in the holes I'd prefer to have those cleaned up and repaired rather than have them unde the carpet. Also some of the holes looked relatively deep.

It's a bit like if you scratch the paint on your car, it's a good idea to touch it up to prevent further damage to the surrounding paintwork. The slab ain't going to fall apart but it's what they should do as tradesman.