KiCad allows overlapping zones to make it easier to have two (or more) zones on the same layer while kicad handles which one gets to fill which area. To do that kicad needs to know which zone should get exclusive right in which area. This is done with priorities (you can have a zone over the full area with low priority and then place smaller zones inside it with high priority. Kicad will then allow you to have these high priority zones with the proper clearances.)
Without you giving priorities kicad has two options:
- fill anyways (current option, gets DRC to complain as it should)
- do not fill (similar result as DRC will complain about unconnected, probably harder to see by users and us as there are other reasons why a zone might not fill.)