I suspect you are using Air Arabia for the cheaper fares...

I've noticed you've posted your question to other website(s)...

It looks like a transit is possible..in these cases, but you should ask Air Arabia to help facilitate..

http://www.shj-airport.gov.ae/transferandtransit.htm

If you get there, someone sympathetic might help -- or might not..so you don't want to get there without a status.

Rasheed