Yes, if someone gets employer contributions in a year that are equal to their 415(c) limit of the lesser of 100% of pay or $72,000, then any and all deferrals would be deemed catch-up contributions.
In your example, the person could actually have had compensation of $72,000, an employer contribution of $72,000, and $8,000 in catch-up contributions.
@SSRRS
Did you file using third party software (FIS, FTW, etc...)?
Did you get an AckID, or did this prevent you from actually getting it filed?
While I agree it sounds like an error on their end, it will probably take quite a bit of back and forth to get it resolved.