First: Is it more important the world-building for this story be emotionally true or structurally true.
The rules within the story need to be consistent, but it's fine to have a fairly light, flexible magic system. I tend to go to pretty 'hard' magic with lots of rules, but one of my stories magic is very symbolic because that's it's role in the story. It's there to invoke emotional themes, and the 'rules' are designed to feed those themes, not make a textbook.
If you decide to go more rules heavy, I feel like one of the first big questions is 'what is magic'. Where does the energy come from? Who/what can harness it and why? Even if the magic is being channeled in wildly different ways, understanding a source (or multiple sources) can avoid problems.
When you hit a problem, I think it's one of the best chances to worldbuild! It's pretty obvious when a writing is panickedly addressing perceived criticism, but it can also lead to really cool answers. For example, let's say you've realized your magic makes it REALLY easy to counterfeit money
Bad Fix - Hurriedly say the coins are magic proof because Reasons, even if those reasons don't fit the magic and make more questions
Good Fix - Think of it as a societal change. If the society has always had magic, think seriously about how it would change how an economy worked. What is valued, what is needed, how trade and social responsibility are viewed! Look at societies that operate without currency, or use written logs for currency. If the magic is new, you can ask "how would a society deal with hard currency suddenly losing all value without technology to fall back on". From there, you can work out.
For things with dragons, what adaptations might they have to protect their lifecycle? Symbiotic species relationships are a thing that exist in the real world, and are completely plausible.
Secondly, sometimes things have to go. Sometimes I really love two ideas that just do not fit, and I have to pick which one works.