Difference between a word combination "retail fuel company" or "fuel retail company."

I would say that "Fuel retail company" is clearly a company that sells fuel at retail level (ie to the end customer, the driver). This is because "fuel retail" can only mean the selling of fuel.

However "Retail fuel" sounds like it could be using "retail" as an adjective to describe a type of fuel that is intended for retail. A "retail fuel company" could therefore mean a company that produces fuel intended for retail.

Or it could just be a mistake!

Sometimes a particular ordering of words may be ambiguous, yet so common and idiomatic that every native knows the intended meaning. For example, "a used car salesman" - everybody knows this means a man who sells used cars and not a "used man" who sells cars. I don't think either of your examples are so common as to be idiomatic and "retail fuel company" would certainly prompt me to check the intended meaning.