> It is not legal to operate a remote transmitter site without [...]

47 CFR § 73.1400(b) permits operation with “a self-monitoring or ATS-monitored and controlled transmission system that, in lieu of contacting a person designated by the licensee, automatically takes the station off the air within three hours of any technical malfunction which is capable of causing interference” (emphasis added).

This doesn’t change the licensee’s basic responsibility “for assuring that at all times the station operates [...] in accordance with the terms of the station authorization,” of course.

> in what ways were they operating noncompliantly?

If the station was off the air and the licensee didn’t notify the FCC within 10 days and seek a silent STA within 30 days, that would violate 47 CFR § 73.1740(a)(4).