There's something wrong with the last npc in the virtual badge quest (West Gearen City). After you defeat any E4 member he asks you whether you want to continue or take a break. If you choose to take a break and then talk to the npc again to continue the quest you are able to skip the part of the event where your team gets replaced with the virtual team and the field is set to glitch field, which will allow you to use your actual team against the virtual E4. On top of that, if you choose to take a break right before the champion, it will reset the whole event and make you start from the first E4 member (the problem with that one seems to be that the league progress variable that is supposed to store how many E4 members you have defeated is set to += 4 instead of being set to 4).