Addition:
Also doesn't matter in which order you do it.
Plot and then water - no go.
Plot and then garden lime, and then water - no go.
Plot and then use Plant Material and then water - no to.

This is still a problem.
Doesn't matter what the garden plot is made with, and doesn't matter what you use to water it with (tried glass bottle, plastic bottle, jerrycan and cooking pot).
Also doesn't matter if you try to water before or after putting seeds down, same problem.
This is on official server 9746 Experimental branch.

This is still an issue, see my first/top-post for all the information - there's LOTS of it.
It's been 9 months and it still happens a couple of times a day atleast.
I see this post is marked as "Need More Info", but no reply asking any question.
The solution by Penta_86 above makes no difference, as I already outlined in my first post.

In T170994#2420142, @Geez wrote:

Hello hyperunknown.
Is this still a problem at the moment? If so, can you please send us a link to your Steam profile? And possibly try to connect to some server and then let us know the server IP/Time of the connection/day on which you have connected so we can check if there is some more info in the logs?
Regards,
Geez

Hello Geez!
I'm not sure if this is the link you need? https://steamcommunity.com/id/hyperunknown/
I'll be sure to jot down the time and date the next time it happens, and reply here with it :D