I believe the steel part of the safe floor was pre-drilled. But the carless safe manufacturer did not make an access hole through the drywall/carpet covered floor for the delivery company to put bolts into cement floor of the house.
I have seen this several times. I have also seen gun safe manufacturers install the gypsum (with precut holes) upside down in the bottom of the safe so that the holes go to steel, and the holes in the steel are covered with the gypsum.
The carpet on the fireproof drywall floor was pulled back and the safe delivery company hacked through the drywall to find the corner holes and put bolts into cement floor and just left this mess under the carpret.
When there's a job that needs to be done, you use what you have available. I carry a hole saw for such occasions, but they must have not had one. I carry a knife that may have cut a cleaner hole, but it looks like they had a screwdriver.
Did they discuss this with you prior to doing it? I don't think it's a big deal either way, but I would have least pointed it out. Your options at that point would have been to let me remove the offending gyspum and bolt it, or leave it as is and not bolt it.
Leaving the mess under the carpet is also typical. Unless the customer is offering us the use of a shop vac, I don't have one on the truck. We drill, bolt, and cover. The dust stays right where it is, and short of looking for it, you'll never see it since it's covered.
Should I get some drywall and insulation and just fill the holes?
Are the holes causing some problem aside from you being upset about them? It it will make you feel better, sure. Otherwise they will have no impact on the function of the safe.
I need help as I no longer trust the safe company.
Are they a safe company, or just some outfit that sells gun safes. There's a big difference. Either way, I don't see any reason not to trust them. If anything, you shouldn't trust the manufacturer. They seem to be the ones that screwed up.