ok i feel like you're trying to use commands that are not in the list of commands of minecraft or the commands that are part of plugins.
for example :
[11:13:05] [Server thread/INFO]: gejmricek issued server command: /vanish
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[11:13:09] [Server thread/INFO]: gejmricek issued server command: /vanish gejmricek
i dont think there is a vanish command in the plugins that youve installed thats why they are not getting executed.
But when you tried to change the time using /time set command worked because it is a default minecraft command.
Here are the list of minecraftcommands
Commands
Commands, also known as console commands and slash commands, are advanced features activated by typing certain strings of text. In the client, commands are…
minecraft.fandom.com
Like the system says type /help <pluginname> to get the list of commands supported by the plugin