Maybe it depends on specifics. Mint must have some heuristics that attempt to discern whether or not a transaction is a symmetric internal transfer and they work for some and not for others. It's not an easy problem, given the zillion variables and different banks etc. but after all these years and witnessing the choices they've made on where to allocate resources it's hard to give them the benefit of the doubt.

If you keep categorizing transaction from, say, checking to credit card or savings to checking as transfers it'll pick up on it after a bit and automatically categorize them.