2 come to mind that still haunt me today! They both happened when I first started getting into retro gaming.

Bomberman 2 - NES - Saw it for $7, but I'm not a big bomberman fan so I decided not to pick it up, I found out later that day that it was selling for around $70, I tried going back to get it, and it had sold already.

Wacky Races - NES - Saw 2 copies in the same store each for under $10, I had no idea they were rare until months later and by then they were long gone... haven't seen a copy since. They are on ebay around $100.

Since these 2 situations I bought NES and SNES rarity guides on my phone so I always know