I still haven't been able to reproduce the bug on my end and I'm starting to go a little crazy. I was beginning to wonder if I had already done something in my end that fixed it without realizing, so I downloaded the same 1.2 Alpha that everyone else has and started looking at the code there. I still have no idea how this is happening so I just wanted to clarify what I'm looking for.
(Spoilers for anyone reading this before playing the game, you have been warned)
When you say "The MC showed their partner pokemon to Cynthia twice, the second time happened even after it evolved," exactly which scene is it that happens twice? Is it the scene where you're chatting with Cynthia back at the hotel in the evening? Or is it the scene where you go up to Cynthia's suite to get TM's for Metang? Or is it two different scenes but both of them act like you haven't shown your pokemon to Cynthia before?
If it's the same scene twice - when does the scene show up? It should be the first scene you see when you go and get drinks with Cynthia for the first time, and nowhere else. When it shows up for a second time - what day/time is it? Does it happen on Day 2/Tuesday, or on Day 3/Wednesday, or on Day 4/Thursday? Does the scene play at the end of the day at the hotel, or is it popping up at some other point during the story? What happens after the scene?