And why as Muscovy I keep getting Subjugate Kazan AND Subjugate Crimea at the same time, which effectively leaves me with just one mission? Where are those regarding HRE (before you ask: I'm Catholic and the Emperor) and many others?
Obviously, if the player (for some reason) indeed wants to expand eastward early game, then he can take either of these, complete and then pick the next one. If on the other hand neither of these is within his scope of interest, then they two are just a ballast, cutting possible options drastically.
[HUGE MUSCOVY PLAYER HERE, 2165 hrs in the game recorded and probably 2/5 of it was Muscovy if not more.]
With the missions, i think it just goes with whatever you can/should do ATM. I've seen them both at the same time before, and after picking one and fighting-finishing the war i canceled the mission and was still given the option to take the other one, and later on STILL got the mission to get the one i took 1st. So long as the conditions for it are meet, it will come up.
I know for a fact cuz I've always(if/when i remember) canceled the mission after the 1st war, unless I plan on annexing them in 2 wars, and always got the mission back later.
The only thing that changes is the province that gets the reward, which is ALWAYS the capital of the nation your conquering when taking the mission. So if you take the Mission for Kazan and cancel it after the 1st war, the next time you take it, the boost will be for their new capital.
EDIT____
Did you mean they literally they have 2 missions selected and active at the same time? Because that would be weird if true and a bug i think.