I was following this guide to get to Shaymin and after saving by talking to the Pokemon Center nurse and soft resetting (skip to around 9 minutes), I was supposed to end up in the Mystery Zone. However, when I reloaded (by both closing out of the game and by soft resetting), I ended up on Newmoon Island. I was able to correct the glitch using the video and attempt the glitch from scratch, which got me to Shaymin, but I'm curious about why this happened.
I had previously used this glitch to get to Darkrai so I'm assuming that had something to do with it, so is that why this happened or is there something else I'm missing?