"Cross League" fixtures essentially get associated to EVERY division that either of the teams playing are in.  So for example, if you have Team A in division 1 and Team B in division 2 and you create a cross league fixture between these two teams, the fixture gets associated to both those divisions, and therefore shows up in the list twice. 

However, in the example above, there is no real reason for this fixture to be set as "Cross League" - as it is not, strictly speaking, cross league.  It is just cross division.  So you can create this fixture by just selecting the league, and the season and leaving the division blank - that way, the teams available to play that fixture will be ALL the teams in the league.  In that case, the fixture would only be associated to that particular league/season and would only show up in the list once.

Cross league fixtures are for just that - fixture that are between two teams in completely different leagues.  And once the cross league fixture has been created, it will show up in the fixture list for both of those leagues.