Yeah, you could line up the holes wrong, but even that will be difficult.
The hole in the gas block is intentionally over sized. There is a stop on the barrel preventing the gas block from being pressed on too far. If a pinned gas block is used, it's impossible to get it misaligned. Even if a non pinned block is used, as long as it's pretty close to straight up, it will work fine.
I have tested this theory with my own gun. I installed a gas block that uses set screws. I moved the block about 2° left and right. I then moved it forward, off the stop, a little. I did all this to see how this misalignment would affect the operation of the gun. To my surprise, the gun worked with the gas block in all these positions.
Can it be misaligned? Sure, but it will have to be obviously out of place to cause a malfunction.