UPDATE (June 29, 2018): This may come of no use if i am sure because of the recent 1.7 update 3 months ago. you can use the /repair command to try to pop these things. if that doesn’t work then try this.
Edit (June 30, 2018): At the time of editing please do not dredge this thread up as it may be quite old if you are seeing this a few months or later. or if you are from 2020
Got these annoying things? You came to the right place but I recommend you use wood for this trick.
Place these in front of it
Place a door on the trapdoor
Destroy the door at the bottom where the trapdoor is located and it should pop off easily.
This one might be not as tricky as the other one but we’ll get through it.
Place a wood block below it
Place a door on the wood
And then buy yourself an ember
Then you should be done and in my calculations if you get this right you should be glitch free in your world.
I hope this helped you out and have fun with your nice world but if I get complaints that this doesn’t work I will update this thread.