Hey

Usually, this can stem from an error in connection.
Is it possible to emulate the bug in a video?

I can't record a video atm, I admit there is a connection problem in my country because AAG cable is currently broken. But this problem was there even before AAG cable went down.
I'll try to record a video about this bug asap.

This happens a lot to me actually. It's near the end of the fight, so I never really bothered with it, but it does happen to me as well. It only started after the 2.0 update.

Hello.
This might be a problem due to the x2 battle speed.
I have noticed similar situations too.
I think there is a short time limit for you to press the skill *on. If you are late, then even if you hit the skill *on it wont go in the same round. This time limit is even smaller during x2 speed (since battle is going at a relative higher speed), making it even harder to press the skill.
Try fighting in x1 speed and see if it happens still.

that is for normal connection though. If there is some kind of lag, this has a higher chance of occurring too.

As for example where it can happen, let's see:
If you run the typical Scarlet-Anko lineup in nine tail and try to use anko in 3rd round after everyone's standard, sometimes it wont go if you are a little late.

another wierd examplt might be:
In hanzo SA, let's say you are running Scarlet-Sasuke-sai-sakura team. If you use sasuke in round 1 after his standard, and then use him during shizune round 2, c*e him immediately again in the same round, if the speed is in x1. With x2 speed battle progress too quickly to do this.

I know these aren't the best examples to give, just the one that came to mind at the moment.

TL; DR don't use 2x outside of fox, and cast everything half an action early.

2x would cause this yes.
The thing that happens is something along this line:
You can't use the mystery UNTIL you SEE the chakra gain etc
You can't use the mystery AS SOON AS you are unable to use it "in reality", this include if the round actually ended (note that between the actual end of a round and the start of the round, the game waits for everyone to catch up on animation, which is why there are long delays between turns)
reality is AHEAD of what you see.

Therefore, the order of event goes like this:
You met the requirement to cast in reality
You can no longer cast in reality
You see that you met the requirement(the stuff happened a bit ago) -- but can no longer in reality due to cc, chakra drain, end of round etc.
You eventually see the "cause" of unable to cast (in this case, end of round)

If you hit the keyboard in case it is end of round, it will cast at the start of turn next turn, because that's where "reality" is waiting for you. The game, I believe, gray out the *on because since it is "in reality" next turn, it doesn't want you to cast a mystery using the "previous turn"'s chakra.

So you really shouldn't use 2x outside of fox if you don't plan to simply *on spam everything at start of the turn.

In case of fox, you have to know exactly how many action early you need to cast, depending on your internet speed. For example, I want to keep my barrier up until everything have attacked, as the barrier grant stat boost, but I DO want to release the barrier to use it to deal damage (using garra here, same with haku/anku/sasuke barrier), I click to release it at the START of my THRID character's movement, because that's when, after a number of tries to find out, it will ACTUALLY happen right after my FOURTH char movement but before fox hits (if I do it in the MIDDLE of my THIRD, fox will act first, if I wait for my FOURTH to move, I will be unable to cast it at all)

And no, they can't "fix" 2x, because everyone sees stuff at different speed. To "fix" 2x would imply waiting for everyone to catch up after every single action which requires back and forth pings and potential internet delays, that will entirely defeat the purpose of 2x. In fact, it won't work all that well in live PvP on 1x due to sync reasons. It's hardly justifiable for the entire world to wait on your slow internet after EVERY action, it's bad enough that it happens between turns (I have seen >10 second waits between turns, imagine that for between every action)

My internet at normal speed (without the current broken AAG cable) can download pretty much from all common host like google at >2mb/s. I don't think my connection is slow as you said. Back when I first started this game the problem was never there but it appeared like 2 months ago.
Even when 1x pvp in sage or arena this sometimes happen, rarely but it still happen.
So I think there was something changed in their server setup, not my internet connection.