Similar thing happened with my Orange 5, was very very specific about which bit’s needed protecting. Brake mounts, bottom bracket, headset, swingarm mounts.
They didn’t do any!
Had the bb refaced, headset wasn’t a problem, brake faces are ok, had a nightmare with swingarm, very slowly dremeled surface.
All good now and finish is great, but big lessons to be learned, leave bolts in bits you want protecting, old bb etc.
Absolutely no use marking stuff as it’s probably going to be blasted off anyway.