First the obvious troubleshooting disclaimer:
UI issues occasionally pop up after game updates. The developer recommends players experiencing issues with their UI use the "Reset UI Position" and "Reset UI scale" buttons in Options > UI Settings.

More specifically to your issue, the only way we can reproduce what you are seeing is when we spread our skills out to other Skill Shortcut Trays and flip between them during combat.

1. Place a set of skills on Tray 1 and another on Tray 2
Tray 1
Tray 2

2. Use the skills on Tray 1 so that they appear on your cooldown bar
3. Switch to Tray 2 and use those skills
4. Now switch between both trays and note the cooldown bar reorganizes and may create skill gaps
Skill Gap

We communicated this issue to the developer Bluehole long before this post. They told us the cooldown bar was only designed to updated off the currently displayed Shortcut Tray. Skills placed on a Tray not displaying or on the extended tray are not tracked.

The dev has not communicated to us any plans to rework this functionality.
Edited by: SingleBear 1 minute ago