Ender Crystals can grief stuff even if the gamerule mobGriefing is set to false, so that people can use 3rd party programs to spawn ender crystals, and they will destroy stuff.

Steps to reproduce:
-Go to the end.
-Find an ender crystal.
-Build something so close to it/around it.
-Make sure the gamerule mobGriefing is set to false.
-When you're done, punch the ender crystal.
-You'll see it destroyed part of your building.