Afternoon,
Who writes and approves the permits? Is the issue definitely the permit, or is the contractor drilling in the wrong place?
I am not 100% of the underlying UK legislation or even if it would apply to your situation, however my understanding is that the owner of the site is the main dutyholder and should be checking whatever contractors are doing, in case it comes back to bite.
If somebody at your company already approves the permits, then they need to explain at least why they aren't physically walking the job and checking, but possibly they should be put in another role because they aren't cut out for that one.
Design drawings should never be trusted and every job ought to be walked. Ensure the company rep has appropriate tools to verify that there are no pipes or cables in the way.
HTH