Vanilla Minecraft commands (/me, /teammsg, /minecraft:help, /w, etc.) no longer respect permissions. This only fails with Vanilla commands, Spigot/Bukkit provided ones behave as expected.
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Replication

• Install a permission handling plugin, Luckperms is the one I used for testing.
  • Alternatively; create a plugin that will assign a player a negated Vanilla command permission.
• Negate a vanilla command's permission, I prefer using `minecraft.command.me`.
• Attempt to execute `/me bloop` command, or whichever command the permission you negated results to.

Expected Result

The command would fail and be removed from the player's "known commands."

Actual Result

The command remains in the player's known commands and is able to be executed by the player.