Maps with "holes"
 

Autogenerated maps frequently have depressions or holes in them, typically like the one here. In my experience, in real terrain there are seldom such depressions. Gullies that lead somewhere, yes, but very seldom isolated depressions. If there are depressions in real terrain, they are usually lakes or swamps. IMHO these maps are annoyingly unrealistic, though I admit they are not a problem for actual play.

Would it be possible to tune the map generator so that it avoided this?

Re: Maps with "holes"
 

As far as I know a hex represents about 50m. So it seems reasonable that an old sinkhole or a disused quarry would look like that ingame.

Re: Maps with "holes"
 

All perfectly normal and entirely deliberate on a few maps ( #183 is one of the best examples of this effect ) but certainly not the majority and I have no intention of removing them. There are AMPLE controls in the game to regenerate maps before you play on them if you don't like the one you get.