Make sure you've done the following:

• You're using the latest build for your server version
• This isn't an issue caused by another plugin (doesn't look caused by it in the stacktrace but it happens since PacketLimiter got installed which listens for all packets)
• You've checked for duplicate issues
• You didn't use /reload

Debug paste link:
https://gist.github.com/b79fa863721a039726fd012f1e303da9

Description and relevant errors:
https://gist.github.com/008dce91562946d744448fc623374000, the first line is spammed a bunch of times. Happens since the PacketLimiter plugin is installed which basically filters all packets which is probably why this has only been noticed now. The server is Origami, my own Paper fork with very slight modifications which should not touch anything packet related at all.

Does this happen with only PacketLimiter installed? And I assume it doesn't happen when it's not installed?