I was going to say "endermen", but they only influence certain blocks. The ones on your lake could do it (particularly if an endermen picked it up, and then you switched to peaceful - that deletes the held block). But I have no explanation for the underground blocks looking like that (especially along chunk borders). I'd expect memory corruption to be more random; if it were corruption of the (compressed) save file it'd manifest as a chunk reset most likely, and in memory it probably wouldn't be there.
This does remind me of the ocasional seed math error that happens where structures are all along one block, but that can only mathematically happen on one axis.
Do run a complete RAM and disk check on your server. That'd help. I hope it is caused by something like that, because really subtle bugs are scary.
https://hub.spigotmc.org/jira/browse/SPIGOT-687
Multiple people cannot reproduce this, and despite there being over 100k servers with Spigot installed, the bug tracker has 3 reports of this issuein as many years.
An issue like this could literally be radiation flipping bits in your computers memory (which isn't nearly as unlikely as it seems), or even poor quality hardware.
https://en.m.wikipedia.org/wiki/Row_hammer
http://lambda-diode.com/opinion/ecc-memory
The more I think about it, the more likely this possibility seems when you are not running your world on an ECC server. Minecraft is somewhat unique in this in that it uses heaps of memory and it is very easy to spot such an error which can easily manifest as a missing block.
Well gee thanks man. If you check the previous thread it also happened to people that didn't have plugins installed. I have tried to uninstall the plugins now. I think Bukkit corrupted the world somehow a long time ago and that is why you can not reproduce the problem in never versions.
Also what do you think of the invisible star glitch or the lightning glitch that is shown in one of the pictures? Have you seen anything like that before, holy crap man its so weird.
Also in the case of the Endermen: We do not have mobs or monsters enabled. And I have been filling the gaps in the beach from time to time those holes in the picture are very recent ones.
Also do you mind checking it off as "not resolved" because it surely isn't but thanks for the help mister Spigot moderator! I am sure more people will come by and comment if you give the thread a bit more life than just a quarter of a day, mister! 
Cannot reproduce this issue and it's clearly not a widespread issue.
It's certainly very unlikely that Spigot itself is pulling out single blocks from your map.
Without widespread reports of this, it is much more likely that it is the fault of a plugin you have installed (heck its so far and few between on the overworld it could be endermen).
I can't really explain the underground stuff, but its clearly note a widespread issue
I wouldn't say it's a duplicate seeing how this problem is in a bigger scale and I have more information to add so we could localize the problem and solve it.
Also I replied to the original thread first but a moderator removed it and told me to create a new thread instead.
And on the fact that it is not reproducable: I disagree. It obviously has something to do with the world being very old even though the server is new. The bug only effects the world when its being hosted by the server.
Looks like a duplicate of SPIGOT-687
And I think it's still unreproducable.