This bug affects version 9.0.10. When PokeStops are used, they are supposed to turn red while their cooldown is in effect. However, this erroneously only happens the first time you open the loot of any given PokeStop. Any subsequent collecting of items from that PokeStop will not result in the PokeStop changing color. Apart from the PokeStop not changing color like it is supposed to, the cooldown itself works as normal.

This affects PokeStops spawned from any method: placed by hand, naturally spawned on waypoints, and spawned with waypoints using structure blocks. This also affects all rarities of PokeStops: common, rare, and legendary. It doesn't matter whether the game was open or closed when the cooldown finished. It also doesn't seem to matter whether the chunk was unloaded at all during the cooldown.

Here is a video showing this bug:
https://imgur.com/a/HJdqipG

How to reproduce:
1) Go into the Pixelmon config folder.
2) Go into the spawning.yml file, scroll to the bottom of it, and change the loot-time under poke-stop from whatever its value is to 1.
3) Save the changes.
4) Start Pixelmon and enter a world.
5) Place down a PokeStop of any kind and right-click (or press your "use" key) on the bottom of the PokeStop to collect the items. Notice that the PokeStop turns red.
6) Wait at least an hour (you can leave the game if you want and do other stuff until the cooldown finishes).
7) Once the cooldown finishes, right-click (or press your "use" key) on the bottom of the PokeStop again to collect the items again. Notice that the PokeStop does not change color.

Tested using The Pixelmon Modpack on CurseForge.

Linked to a internal ticket.