(Warning: Broken English below. So i added images that are self-explanatory... I guess)
As you can see here, I already got all probes scanned, already got the skin, so...
Can't complete this mission!
And in the same save, I unlocked all portals, cores and stuff, but then, when the Mission Compass update came, when I first loaded the game, it auto-completed all related missions to them (except this "Through the Looking Glass", which is a triggered action, I believe)
I think the solution for this is:
If (when this mission appears):
it should check if at least one of the probes was already scanned.
then if (at least one of the probes was already scanned)
Hope this helps!