If you're running a version older than 4.0 than this can be caused by another plugin stopping the removal of entity's. If you have holograms you can't remove and are running on older than 4.0 see the solution here.
If you're running version 4.0 the holograms can be a little buggy and it's recommended to update to 4.1 and use another plugin such as Holographic Displays for handling holograms.
If you're on 4.1+ then the Holograms will be handled by another plugin, either Individual Holograms or Holographic Displays.

The latest version of CratesPlus is currently supported on CraftBukkit/Spigot 1.7.x, 1.8.x, 1.9.x, 1.10.x and 1.11.

We recommend you look at the example configuration file here to see how commands, percentages and other features work.

• /crate settings - Allows you to edit crate winnings in-game
• /crate reload - Reloads CratesPlus config
• /crate create - Create a new crate
• /crate rename - Rename a crate
• /crate delete - Delete a crate
• /crate crate [player] - Get a crate to be placed, place this in a protected area such as the server spawn.
• /crate key [type] - Give the player (or all players) a crate key which can they be opened. Useful for shops and voting systems.

• cratesplus.admin - Access to all /crate commands. Defaults to OP.
• cratesplus.updates - Any player with this permission will be notified of updates. Defaults to OP.