I have LuckPerms Bungee on the bungee proxy and Standard LuckPerms on the Spigot Hub world.
I set the group Admin to have the permission "prefix.10.&l&8[&eAdmin&8]&r" and now it's showing the prefix twice!

This is not LPs fault.
It is most likely caused by whatever Chat plugin you're using.

If you use essentials, make sure you aren't setting the chat format as {prefix}{displayname} as displayname will show prefix/nickname/suffix.