The distinction that comes to mind for me would be that a "rebel city" is rebelling against something outside the city: perhaps there is a king who rules the entire land, but this city doesn't want to be under his rule. A "rebellious city" could be rebelling against something outside itself, but it could also be rebelling against its internal rule (the mayor and the city council, in modern terms).
Unfortunately, this might just be me. I'm not sure that there's any hard and fast rule about this, or if anyone else attaches the same connotations. Would be curious to know.
A rebel city is a city that is ruled by rebels. "The army marched towards the rebel city of York."
A rebellious city is one that is often in disagreement with the real ruler/government. "Three times, the government had tried to collect taxes from York but the rebellious city had refused to pay and riots had now started."