Uh. Thanks a lot (especially for saving my time to get this fixed while spending your own).
That was lightning-fast. 
You can find the fix to the WorldEdit bug in this pull request:
https://github.com/sk89q/WorldEdit-Adapters/pull/5
I spent some time looking into this and I can confirm that it is a bug in WorldEdit's Bukkit adapter and not in fact Spigot.
I know. I hoped that the issue sounds familiar to somebody watching the bug tracker.
If similar results would have existed in either this or WE's bugtracker I would've added the reference. Nevermind, I'll either wait for the issue being fixed "by accident" (which I suppose must have happened in the last releases) or take my own deep dive into it if I have some spare time.
Search text WorldEdit provides no similar results either: https://hub.spigotmc.org/jira/browse/SPIGOT-2361?jql=project%20%3D%20SPIGOT%20AND%20resolution%20%3D%20Fixed%20AND%20text%20~%20%22Worldedit%22%20ORDER%20BY%20created%20DESC%2C%20priority%20ASC%2C%20updated%20DESC
I see no mention of any similar fixed issue. If it is a bug on our end, a minimal reproduction code must be provided.