There are actually two separate issues here I believe.
The first is like the location of Wisbech; there are a few instances of towns being in completely the wrong place. These are errors in the gazetteer data we use. Although we have submitted corrections to this, nothing seems to be happening, so we are considering how we can correct the problem on a town-by-town basis at our end.
The second is minor errors such as the location of the towns adjoining the Menai Strait. Our scenery data, which includes coastlines, is small scale and can be out by as much as 1nm. We don't consider this a problem because our aeronautical data is precise, and that's what we concentrate on, but it does look pretty poor when this can result in town waypoints appearing like they are just sitting in the sea (because the coastline is wrong, usually not the town locations). Alderney airfield is a prime (and embarrassing) example of this, as the airfield appears to be in the sea. This is because our coastline scenery data is slightly offset in the area; our coordinates for the airfield are correct.
The first issue we are in the process of working out how to solve ourselves locally. The second issue stems from the world scenery data we use. Licensing larger-scale scenery data is not currently on the cards I'm afraid, though we do continue to look for the best sources of this data all the time.