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.