I have encountered the same problem and here is what I found out so far:
When travelling in the inter-world space with your ship, there is no sure-fire way to tell if you have already completed a mission that you see in front of you or on the mini-map with the Heartless-symbol.
You can however look at your Gummi mission list by opening your menu and selecting Information > Gummi Records. It will show you the star-rankings of all missions in your current area. That way you can at least see which kind of star-rating the missions have that you still need to find.
In your Gummi mission list, you can tell that you still need a mission that is rated with three red stars. Flying around space, you now know that you can skip anything that has a different star rating than the one you are looking for (e.g. five red stars or three orange stars).
I know that is not very satisfying, but as far as I can tell - there is nothing better the game is offering you.
Gummi missions appear to spawn in the same location every time. So if you keep track of where you already where, you should be able to tell if you already did a certain mission based on their location.