Hi, I was never really into Thouhou, but Bad Apple and others were so much bangers and i've listened to them for year.
I remembered the OG Bad Apple video on Youtube so many years ago to be something like 3 and a half minutes, maybe 3:45 or something. But after I went back to listening a couple of years ago, the song is longer than 4 minutes, and so is the animated video, with a longer instrumental, a longer bridge, and a repeated verse.
The video I watched was the same, uploaded previous to 2010.
This is some form of Mandela Effect that I experienced and I wondered if someone got the same with this same song.
The Mandela Effect does not exist in the manner you're describing, and by priming your audience to expect a specific false memory you're tainting the data from any responses you get.
People wouldn't have the Berenstain/Bernstein thing mixed up in their heads so much if the conversation about it was always phrased as "Who are the authors of that old children's picture book series with the bears?" instead of adding doubt with "Do you remember the authors as Berenstain or Bernstein?"
Bad Apple is supposed to be ~5:24 for the full version. It got famous for its PV (promotional video) which is only 3:49. This is the version which made it popular, and likely what you watched.
Subsequent fans have edited the PV by slowing it down in certain sections so to set it to the full version of the song.
The Mandela effect is likely caused by people mis-rembering things or just generally being mistaken about their memory. Even the most common Berenstain/Bernstein example comes from simple confusion.
Best article i could find with pictures.
https://www.cracked.com/article_34881_sorry-but-there-is-no-berenstain-bears-parallel-universe.html
You were probably so into the song the first time you heard it it was over before you realized it.
Actually going to answer your question here instead if bickering about terminology. Maybe the original song was shorter, and it was extended to match the video and include all the characters? Maybe someone uploaded a "nightcore version" and that's what you remember?