I am having an issue where all commands I type are red, and tab complete isn't working at all. I've gotten rid of all of the plugins and am still having the problem. I asked my host and they said for me to contact you. Here is the latest log of the server starting up without any plugins: https://pastebin.com/vUqMye1n
Multiple people on my server are having the problem, and it doesn't have to do with our chat settings. I am not using a mac, send-namespaced is set to true in spigot.yml. It is a 1.13.2 server. I received my copy of spigot through buildtools, and I have the most recent version titled spigot-1.13.2-R0.1-SNAPSHOT.jar. I am OPed, the commands still work and run, but appear red. The only thing that ever fixed it was completely wiping the server of everything.
This is a big issue because it is extremely difficult for me to work, especially in permissions or even just banning while this issue is occurring. 
If you have any other questions please let me know. My spigot is mmcarson78 and my discord is DoctorBlanket#1801
Update: /fly also seems to be malfunctioning for my mods, and it makes them move forward when they hit the spacebar. Almost like they are bobbing in the air. I don't know if it has anything to do with the commands, but I figured it was worth mentioning.