Problem with VIA and Zones

The term you are looking for is via stitching.
Sadly the current version of KiCad has no direct support for it.
But there is a well documented workaround using single pad footprints.


Why? For what reason would you like this to be filled?
The only valid reason would be to save on edging fluid. But even there you should connect it to gnd if at all possible. (Floating planes can contribute to EMI)