This bug has been partically fixed in 15w49a, it works correctly with doors but both trapdoors and all six fence gates still have the issue.
Still in 15w45a
Still in 15w44b
This may be the same bug I reported yesterday, it isnt block lag but the game doesnt render the door as open or blocks as mined immediately. MC-89355
Still happens in 15w38b
I just recorded it happening once while I was exploring. (in 15w36d)
This just happened to me two times in 15w36d, I dont think it is fixed completely
This also happens with Chorus fruit which is supposed to have a cooldown after eating.
This also happens with witherskulls (in 15w33c)
For some reason you can also not reconnect to the server for a few minutes after you broke it, it fixes itself after a while though and you can play
Something similar to this also happens in the statistics menu, being scrolled down on the first page or being on another page and resizing puts you back to the first page again.
Are you sure that the server is a vanilla one? I just tested this on my local (vanilla) server and nothing happened,
I did exactly what you did on a spigot server before and it crashed too, maybe thats the case?
Still affects 15w50a.