My first game was Alpha Sapphire (a little later than the others on this thread), and I made two major whoopsies while playing for the first time:
Note: Let it be known that I only knew about Pokemon through playing Pixelmon on and off for the last year or two, with no idea of HMs at the time, and had no access to the internet at the time (I was on holiday at a summer house).
1. Obviously, I had heard of Kyogre, and how good of a Pokemon it was. However, I found Kyogre to be helpful in a different way...
"Wow, Kyogre has access to Surf, Waterfall, Dive and Rock Smash? This will be so helpful in Victory Road!"
2. I remember the ORAS elite 4 to be crazy hard, so I went to train to face them again. However, I forgot what their levels actually were, and I didn't want to risk going back in there to check. I trained up my Swampert, Cobalion, Camerupt, Tropius, Latias and Luvdisc all the way to level 100 to be safe.
Also, after ORAS I played through X. As a random encounter, I found a shiny meditite in Connecting Cave. I was so excited that I ran around the house screaming, not noticing the red light flashing on my 3DS. One dead 3DS later, I was so close to resetting, but I didn't want to lose Sid the Froakie.
Skrelp...