If it's something that crosses or hits the fence line you should turn in when doing the outer and make it part of the outer. Then you won't have any issues with the display, SMS, or the machines messing it up. 


Example, a terrace in the middle of the field is an interior boundary you do once the outer is finished for that field. Same with a pond, sinkhole, etc that are islands on their own. 

A waterway that starts in the middle of the field and goes all the way to one of the field edges (and continues on most likely) should be part of the outer. When you come to it while driving the outer, just turn in on the near edge and follow it into the field. You'll end up back on the far side of the waterway and along the fence where you keep going on the outer.