OP please read about change on the bitcoin wiki:
https://en.bitcoin.it/ChangePut simply transactions often have change that has to be sent back to your wallet. For privacy purposes it is better to use separate change addresses. You should leave this option checked. If you leave it unchecked change will be sent back to the address where the input coins came from.
What that page doesn't tell is how there is a conflict with change and network fees.. First think new users are going to do is try and combine change with other change for other transactions..
I can't think of any conflicts. You will lose privacy if you combine multiple change outputs into a single transaction though. Is that what you are referring to?