Stitching is the practice of adding vias between filled zones on adjacent layers of a PCB to assure that everything is at equal potential throughout both zones. This is something you typically do if you have filled (i.e., flooded) the unused spaces on both top and bottom of your board with copper and have connected the floods to ground or some other reference.
The KiCad FAQ outlines a process for doing this, and it works fine until you refill (i.e., re-pour) the zones–or the DRC refills them for you. When the zones are refilled, the vias you added for stitching become isolated from the zones and end up as little pads floating in space.
The problem and a workaround was discussed in a thread on the kicad-users mailing list. Here's a slightly less terse summary of what you need to do:
You can repeat this as many times as you want to create different clusters of stitches. When you refill zones, the vias will retain the connectivity information and work as expected.