I experienced this as well. I moved a large 91 block diameter glass block dome with the clone command and force parameter. I then used the fill command to clear away the leftover blocks from using the clone command to move it. After leaving the chunks where the dome is and then returning, some of the leftover blocks I had cleared away had reappeared. I then clear them away manually block by block and it still happens after leaving and returning to these chunks. I did this 2-3 times and finally gave up. Also this happened in the overworld for me rather than in the end.
MCPE 1.0 crashed the other day on me while playing offline and the issue only resolved after connecting to Wi-Fi. I play on a Wi-Fi only iPad Air 2 with iOS 10.2.
This was an odd experience considering I often play on my iPad without an internet connection.
Oh and I experienced it in MCPE 1.0.2.