I believe the answer is no, if you're worrying about Crucial Elements, you should make sure the MC Crucial Element is an element of the MC, and IC Crucial Element for the IC. (I say "if" because Narrative First has some articles mentioning that you can probably not worry about the Crucial Elements, especially in first draft, and they'll still turn out okay.)
I can see why it may seem strange for your story. What it's saying is that in the OS Throughline, the MC (or more accurately, the player who is the MC in the MC Throughline) is motivated by Control. This might be an inner need, something that makes him tick or could give him peace; something he may not be aware of. This is in addition to, and separate from, the fact that in the MC Throughline "something to do with Uncontrolled" is what drives him and causes him problems, while "something to do with Control" would resolve his personal problems.
The reason your Crucial Elements are set up that way is because your story has an Outcome of Failure. If your MC could "jump" to Control and that solved both the OS and the MC Throughlines, you'd have a Success/Good, not a Failure/Good.
So I think all it's telling you is that the way he adopts a solution of Control for his personal problems, means he kind of uses up that Control so he can't use it to solve the OS problem for everyone.
(I think if you can really visualize your throughlines as separate stories of their own, it will help to understand how this works. If the MC's personal problems are too much the same as the OS problems, then it's hard to see how it can work properly.)