Worst mistake to ever make in the Pokémon world...

[Kitt]

Mistaking Rayquaza as the almight Shenron and asking him to grant you a wish.

[Dorchadas]

Mistaking Rayquaza as the almight Shenron and asking him to grant you a wish.

I thought you didn't like trolls.

[SirBlaziken]

Telling 'yo momma' jokes to a cubone

[Mockery for One]

A BIG mistake would be being a dinosaur and going to the Pokemon World...

Trust me, EVERYONE will mistake you for a rare unseen Pokemon.

[Kitt]

Battling an Officer with a Parasect holding Big Mushroom....

[Mockery for One]

The mistake of the year would be to mention being a fan of Digimon, BEYBlades, Kaijudo, Redakai, or any ripoff.

[DisturbedHaxorus]

Killing a Magikarp and letting its siblings survive. It may take a few years, but you and everything you know will be reduced to streaming piles of ash and sea-dragon feces 

[Mockery for One]

Releasing an absolutely PERFECT shiny Pokemon.

[JES]

 Raising a Timid Riolu into a Lucario without teaching him Nasty Plot, not realizing that only Riolu can learn Nasty Plot, not and Lucario.

Taunting a Primeape because he is locked into a fighting move, and can't touch your Mega Gengar.

If he ever sees you again, and he gets the chance, he might bash your face in, trainer's commands be damned!

For that matter, using Taunt on a Primeape, period.

Battling near a Beedrill's nest. Especially with a Pokémon that can't defend itself very well. And freezing up, and failing to recall him right away.

Challenging a crime syndicate with under-leveled, inferior Pokémon. If they beat your Pokémon, you and your little friends will be sleeping with the fishes, or otherwise slaughtered execution style.

Asking your Hypno to babysit your kids. Unless you also have a Dark or Ghost type that will keep Hypno from getting any ideas. Except for Gengar, because if he is goofing off, and Hypno ambushes him first, Hypno will have free rein of the house. Gengar is many things, but durable is not one of them.

[Kitt]

Having a keystone and using Rayquazite on a Charizard to get Char X.

[Captain Jigglypuff]

Having a keystone and using Rayquazite on a Charizard to get Char X.

Rayquaza doesn't need a Key Stone to Mega Evolve.

[Kitt]

Rayquaza doesn't need a Key Stone to Mega Evolve.

Which is why its a mistake. XD Double mistakes.
1. Using a keystone to mega evolve the wrong pokemon.
2. using the wrong mega stone.

[Mockery for One]

Another mistake would be taking your Pokemon who gets any sort of panic attack (headaches or whatnot) around Mega Evolutionary topics to the place that seems to depict Mega Evolving the most: Sky Pillar.

Desiree would like a word with you.

[JES]

 Leaving ALL of your Pokémon with Nurse Joy during a night stay. A reference to this CreepyPasta: https://www.youtube.com/watch?v=b8ii3E9mxU0.

Yeah, I always keep a Lv. 100 or Ghost type (especially one of my Gengars, because they love to party ALL NIGHT!) on me, just in case.

[SirBlaziken]

Unless you also have a Dark or Ghost type that will keep Hypno from getting any ideas.

Or anything that is a bug type, imagine Hypno shrieking at a wurmple.