I think it is probably a result of shared boundary ways that are included in the relations, like http://www.openstreetmap.org/way/362763546 Which is a member of Spain, Portugal and several lesser boundaries.boundaries. Edit: Actually, it sounds like this is the issue: http://wiki.openstreetmap.org/wiki/Talk:Osmfilter#Drop_specific_dependencies There are relations included as members of the Spain relation. If I understand correctly, osmfilter does not do what I speculated above, it resolves subordinate dependencies only, it doesn't seek out parents of included objects.

I think it is probably a result of shared boundary ways that are included in the relations, like http://www.openstreetmap.org/way/362763546 Which is a member of Spain, Portugal and several lesser boundaries.