I inspected a sub panel fed with a number 4 copper cable. The main panel breaker was a 90 amp breaker, but the sub panel breaker was a 100 amp breaker. Is this OK?

Sure, a bit odd , but the 100 amp cable and downstream breaker is now protected at 90 amps. Any overload at the sub panel will cause the 90 amp Cb to trip, while the 100 amp Cb will remain closed.

#4 copper is allowed by NEC code as a 100 amp residential only feeder.