Trying to use the ClassicMotd will add [Line, Line] to the motd:

Also using empty slots in RestrictedMode gives []

I've disabled the ClassicMotd, this does not happen in random motds.

Can you share your config.yml?

https://pastebin.com/Dd6QGZxR

Your config is absolutely fucked in many places. Let me fix this up and see if I can reproduce the described problems.

Ok, good news. You only messed up your config. Here is a fixed version: https://pastebin.com/CEsf6Rp9

Things you have to look out for:

• Bullet points, like -, are only allowed in RandomMOTD and HoverText. In all other places, only a single string is allowed.
• You can use %line% only one time. A server motd can only have TWO lines total. You were trying three sometimes.
• Don't add line breaks, e.g. via enter, in front of a %line%. YAML doesn't like that.

When in doubt, have a look at the default config or the wiki describing the most important things.

Let me know if this fixed your problems.

I was about to tell you this bc i checked the original config and ClassicMotd doesn't support multiple entries
I believe i you can do this too:
include_newlines: |
exactly as you see
will appear these three
lines of poetry

fold_newlines: >
this is really a
single line of text
despite appearances

Yeah, don't really care about that. Are your problems fixed?

Yes