In the case of buttons (the unit icons in a build queue are buttons): the interaction triggers when the click is released, not when it is pressed down for the first time. Meaning: if you right click to remove an order and before you're done 'clicking' your mouse leaves the button then you effectively didn't remove the order simply because it didn't register as a click.
I can only imagine that as the game goes on you'll likely want to issue orders faster. And by doing so you may move too fast or click too slow. This is a common 'bug' that is not actually a bug; it's how all buttons work even those in Windows.
With regards to path finding - do you have specific moments when this occurs (replays + timestamps)?