This is a pin on a D-sub connector, connected to a Gnd fill.
What’s the best way to manually tidy up the extra connection?
Probably easiest to do a Rule Area (Keep Out area) and set it to keep out fills . . .
Another easy way is to draw one or more tracks form the “into” the zone, (and lock it to be sure it stays there) and thus do it manually. KiCad does not generate thermal spokes for pads that are already connected by tracks. There is no generic “best way”. The solution should match the problem in each case.