Though it looks like a trace, it goes away when I press control-b and re-render the 3D board. Is this just a quirk that happens with the 3D model, or is something more worrisome happening, and will I need to worry about it if I order the board to be fabbed?
To be honest I have noticed the same and had the same concerns. @straubm is right. The Gerbers are the source of truth. In the end my boards, in my case, came back OK from the fab. So this is just a quirk with the 3D render.
There are other quirks, too. So some tented vias are shown untented in the 3D renderer although they are correctly shown tented in a gerber viewer. Unless you have selected “do not tent vias” in the plotter, of course.
The clearance setting (of a zone) determines the distance between copper features of different nets. (example between gnd and any of your signals)
The clearance you can use is determined by your manufacturers capabilities and by the voltage you board is used for.
In the picture you posted there is quite a large distance between the zone and the tracks on your board.
You can change the clearance settings of your zone by pressing e while your mouse hovers above the outline of the zone. (On the left side of the properties window there are 2 settings. Clearance and minimum width.)
Normally you can set this stuff equal to what you use for everything else.
Again, check what your manufacturer is capable of. But i’m sure the standard settings for zones is much larger than what any normal fab can do.
(Zones start with approximately double to what the standard drc settings are.)
As far as i remember this tutorial explains these stuff quite well:
6 mil minimum trace width
6 mil minimum spacing (this is your minimum clearance)
at least 15 mil clearances from traces to the edge of the board
13 mil minimum drill size
7 mil minimum annular ring
There is no maximum. but small clearance means you could get connections where now there is no connection possible. This could significantly influence the ac behavior of your board. (could result in a shorter current return paths)