Currently misteries can be made uninterruptable due to how the game is coded.

No, no, i am talking about every skill, also non prompt ones (even if these are more limited). Manual Interruption purpose currently is meant only to break a mystery that's at the bottom of a queue, not a mystery that is at the top of the queue (aka using two or more mysteries at the same time and trying to interrupt the 2nd or 3rd). Right now you can manually interrupt a mystery that's at the top of the queue only if the enemy uses it as soon as possible before a standard attack action and you don't lag or if you aren't watching a long combo or animation. If the enemy uses the mystery a fraction of second before the set by server time for a standard attack you can interrupt it only if you were on auto mode during that specific frame of time, thing almost impossible to do if not by trying to guess before which standard attack he will use it, otherwise the automode will just use the mystery by selecting the lowest hp enemy.

The mysteries with interruption immunity just won't get removed by the queue even if you are able to interrupt them.

Edit: I'll try to be clearer so you may bettee understand how it works. The battle feature have by the server set timings for standard attacks. So that if you are at 1x speed the fastest 1st prompt move ninja standard attack moves 3 seconds after all the buffs and clones are displayed, then after 3 more seconds moves the slowest first prompt move ninja, then after 3 more seconds move the fastest 2nd prompt move ninja and so on until the round is over.

These timings are fully managed by the server and do not get modified in any way by your actions (client side).

When you manually use a mystery the client sends an input to the server and the server shows the mystery before the following standard action it calculated. Lets say your enemy uses a mystery after the fastest first prompt move ninja moved and you don't lag much. The server let the mystery resolve very likely 1 second after the moment it gets the input and put it before or after the following standard attack depending on the calculations it does for when the following standard attack had to resolve. Lets say the enemy uses it 1 second after the previous standard attack. What happens at that point is that the mystery icon have just 2 seconds to appear on your client side because regardless what you do the following standard attack will be used after these two seconds and you can interrupt a mystery only before it resolves. In this case the mystery icon pops up on your enemy ninja head and you have 1 second to use your own to stop it and if you are ready to do it you are able to let the server understand you want your mystery to be placed in the queue with your enemy's one and if you own initiative your one moves first and the interruption is successful.

But what happens if your enemy doesn't use his mystery after 1 second, but after 1.5 seconds? That the server register it to resolve 0.5 seconds before the slowest first prompt move standard attack and just gives you 0.5 seconds to reply. So when you see the mystery icon popping up you use your mystery, but the server thinks you want to use it after the slowest 1st prompt move standard attack action and not before, because it registers your mystery to resolve 1 second after, so 0.5 seconds after the standard attack (just want to add that if the enemy is able to use a mystery even closer to the standard attack you don't even see at all the mystery icon popping up).

That's how it works currently. I just used time frames you can understand so that you can get the grasp of it, the real timings aren't exactly the 3 and 1 second i talked about in the previous example.