There were three points at the very start of the game where I was forced to completely start my save file over, all three of these points seemed to happen right after I saved the game and after I turned my game off it made it to where I couldn't continue with the game, the first time was right after I chose my starter and was heading to the next town there was a cutscene where I had to stop a Pokemon from attacking two people and that cutscene didn't play and if I was to interact with the characters I would just be given bad eggs, so I had to restart the game.
The second point was when I was heading to get the Pokedex from another professor after I got the pokedethe had asked me to come along and help him get through Milkshake forest, I saved before entering the forest so I could catch more pokemon as I went to the route before to catch some Pokemon and when I went back to the town which was connected to milkshake forest the two guards who stop you from entering the forest shown back up making me have to restart my game again. The third point was when I had to either capture or defeat a mudkip and I saved before hand to try to capture it and when I reloaded my save file when I tried to interact with the mudkip it wouldn't start the wild encounter all it would do was have a exclamation point above it's head, then when I went to talk to the guy who needed my help he only says that he needs help with the mudkip so I'll have to start my game again.
TL;DR be careful where you save the game at because it seems you'll be having to start the game all over a lot.