Traveling to Nether glitches Overworld

Ive had two worlds now that this has happened on. My original one I glitched to the top of the nether and built a gold farm up there so I attributed the glitching to that, but when it started in my second world I got scared because I didnt want this to be a permanent thing. I went to the nether 3 or 4 times and then I came back to the overworld and went to do some exploring and a part of my overworld had been clone and then a part had been taken out in a square. Ill include attatchments.