When setting a players prefix, it only shows up for the player that I set the prefix on. Shouldn't it do it for all players online?

You're setting the player prefix using:
/ne prefix Player '[Tag]'

If so, this specific for only that player. However, the player should see his tag in tab list (If enabled) and normal users will see his tag as well.

If users have the same tag you want to setup groups and provide a permission node in your permissions file.

If the issue still persists, please provide:

• Spigot Version (/version)
• List of Plugins (/plugins)

I forgot to mention that this is using the API. I currently have 4 plugins installed:

AAC
ProtocolLib
NeolyteHub (My custom hub plugin)
Nametagedit

Are you setting the tag on Join? e.g. PlayerJoinEvent?

Yes of course. And before you ask, the listeners are registered.

https://github.com/sgtcaze/NametagEdit/blob/master/src/main/java/com/nametagedit/plugin/NametagHandler.java#L149

We send teams on clear the player's tags in the PlayerJoinEvent. Notice how we have this set to the highest priority. You are calling the API methods too early. Try placing this on a 1 tick delay and see if that fixes anything.

Another guy had a similar problem, the delay resolved it.

Thanks. Will try and get back to you. :)

Worked! Thanks for your help.