Working at a third part vendor I don't technically use Yardi. However, as we Integrate with Yardi frequently we see a lot of things that cause problems for the built in integration process in Yardi.
-Occupant counts. If you are using 3rd party vendors for utility or other billing and base it on occupant counts all occupants in a unit have to be entered into Yardi and marked as an occupant. If you don't, or if you mark occs using a custom field, your billing is going to be more difficult.
-Transfers. Yardi has a built in process for transfers, that many people seem to get wrong. Using the standard method of transferring a resident within Yardi will make things much simpler.
-Notes in the name field. Not a good idea if you are integrating with any third party vendor that bills your residents. If you put notes in the name field and no one notices, those notes are going to end up on a bill or other document that your resident receives.
Those are the ones that come straight to mind. If I think of others I'll come back and add.