The reason is linked to how standard attack mechanics, mystery mechanics and server response are linked together. Basically a mystery becomes uninterruptable if is used very close to a certain standard attack and the server have not the time to understand that you want to counter it before that standard attack.

No, it's about lag.

The fact of the matter is, the game plays at the pace it is at on the server side, which you might be lagging behind. And if so, when the enemy queues a skill (they might also be lagging behind btw), the skill queue will NOT show up until you reach the point in battle at which the server receives the order. The problem is, since you are behind, at that point the server is further into the future, at a point where the mystery have ALREADY happened. Therefore, you can't interrupt it.

The primary cause of this delay is chase chains. The server does not wait sufficiently long for a chase to resolve, usually only about 1.5s. As it were, most chase chains take longer, and at that point you are "behind" the server.

You can experiment this by having two PCs side by side and have two chars in one team (I would recommend throw-away alts for the purpose of experiment. Otherwise it would breach terms of use) If you fight Team instance with those on 2x speed. If you queue a skill on one of them in the middle of a round and observe what happens on the other, you will see that the mystery mark does not show up until much later after the time at which you clicked the *on--right before it is used.

You can dig the forum a little for my previous explanations of those, some of which I've written timelines about... It's... quite tedious and complicated.