I am uncertain if anyone else has experienced this bug, but it is extremely disrupting to my gameplay and has had dire consequences on my raiding.
Please view this minute long video that demonstrates the issue I am having.
(I chose Ninja because it is most visible on the mudra, however it affects all of my classes: Paladin and Astrologian)
https://youtu.be/Cy2f1Gbb4DI
Summary:
When the cool down reaches zero, and the skill is available to be used again, upon execution the countdown resets to 2-3 seconds. You can see the skill is activated visually, but gets cancelled. Upon waiting for the countdown to finish again, the skill then becomes usable as normal.
This is extremely disruptive and I hope it can be resolved quickly.