As of 1.02 update you can now see on the world map if you have beaten a skirmish or not. If it's blue then you have beaten it, if it's orange then you haven't.
Skirmishes cycle around every time you enter a new area. Areas usually only have 2 available skirmishes at any one time.
I'd recommend doing any skirmishes you come across during the main story to save the tedium of doing them in post game. Some are only available in post game and you'll need a team of level 45+ to beat them without too much difficulty.
One spot to keep checking regularly would be right outside Evermore as there are seven invasions and the next one won't show up until you've beaten the one before.