Auto routers is not always working well, even the very pricey ones. Auto routers are often used by people who do not know how. They do a bad part layout and think the auto router will fix all.

I think if you did not have a poly fill on it would have put traces in and then if you added the "polygon gnd" over the top. I think because it started with ground everywhere it assumed that ground could be reached easy.

You need to name the via. Use "gnd". When the via has the same net name as the polygon area fill they will connect.