This is probably due to the way the coordinates are formatted in the wikipedia article. If you want it to be fixed fast, just go to the articles which are not shown on PE, and copy the source of the coordinates and post it here. The, geomagik can integrate it into the next data treatment.
nounours
Example ( I did not check if this articles are shown in PE or not)
https://nl.wikipedia.org/wiki/Leuven
{{Coor title dms|50|52|39|N|4|42|16|E|region:BE_type:city(89910)}}
https://nl.wikipedia.org/wiki/Amsterdam
{{Coor title dms|52|22|0|N|4|54|0|E|type:city(743027)_region:NL}}