Work/entry permit rejection by ministry (MOL / MOI) in uae is very common.
My husband work visa for engineer was rejected for 6 times n approved on 7th time... And it was all very frustrating n disappointing....but It happens .... Ministry reject your visa permit for any minor reason like spell mistake, photo not clear, or passport copy is not in format... In our case that was the reason they wanted passport first and last page copy on same paper but our employer used to upload separate photocopy of first and last page of passport.
In such cases our employer should be strong enough to handle this.
Ask your employer to keep re applying. If rejection frequently then company's PRO should personally go to immi. n can get to know the reason.