1 I can't see a particular ground's marker
On a wide view when grounds are very close together (e.g. Liverpool and Everton) the markers may overlap. Simply select the relevent region to narrow in the view or use the map controls to zoom in further.
2 Is Wembley on the map?
Any ground not in a specific division such as Wembley or the Millenium Stadium can be shown via the 'All Divisions' option in the 'Divisions' dropdown or it can be selected from the 'Clubs' dropdown.
3 Does the map show the start or end of the season?
The map shows the position as at the start of each season.