"This is 9.99 yuan."
Probably depends upon the interpretation of the English. In the context that you are handing over $9.99 and you say "This is $9.99" then that would be "這是九塊..."
But in the context that you're saying for the price of something "How much is this?" "This is $9.99" then you're really saying "This costs $9.99" and that is probably where the approved answer "這個九塊..." comes from.
The only time you are likely to end up with fen is when you change money because it can come to an odd amount. Once you have fen it's very hard to spend them. Somewhere I actually have some fen NOTES that I got from a bank in Guiyang. They are tiny and not as pretty as the yuan and mao notes. I also have a few 5分 coins which are like aluminium half pennies.