If EssentialsX is installed some normal commands stop working. For example the scoreboard command and the "@e" or "@p" target selector

[16:29:50 INFO]: > kill @e
[16:29:50 INFO]: CONSOLE issued server command: /kill @e
[16:29:50 INFO]: Error: Player not found.

[16:30:03 INFO]: > scoreboard
[16:30:03 INFO]: Unknown command
[16:30:03 INFO]: ...scoreboard<--[HERE]

In 1.13+, vanilla commands don't work unless you type the full syntax - you need to type valid arguments after scoreboard for it to work.

For /kill, EssentialsX includes its own version of the command - to use the vanilla version, either use /minecraft:kill or override /kill with /minecraft:kill.