This one I found is...weird, if you will. I'm not even sure if this counts as a glitch, but here's what I found.
I was to retrieve a Calcium from a Stunky in the Sky Stairway for a Blissey. At the 47th floor, I encountered the Stunky. After my Charizard partner, Hanaela, defeated the Stunky, it exploded with its Aftermath. The Calcium was nowhere to be seen, and it wasn't said that I cleared the mission. So I went through the rest of the Sky Stairway and ended my day. After waking up at the Sharpedo Bluff, I thought I could take the job again, but the job disappeared from my job list, as if I cleared it! But I didn't...
I actually found that job on the Outlaw Notice Board, I didn't use a Wondermail code to get it.
EDIT: This was from my Explorers of Time game, by the way ^^;
And to do this, you need to bring a Pokemon with Damp as an ability, such as Quagsire.
Anyways, this isn't really a glitch as much as it was poor placement. I stepped on a whirlwind trap thing, and got blown between two non-connected walls, and got stuck there, and had to turn off my DS to not lose the good items I had :[
In an image..
http://i38.*******.com/2mi43nk.png
sad
I don't know if this was a glitch or just a really rare occurrence, but... I got a dungeon shopkeeper Kecleon to stalk my Lanturn in EoT. A wild Weezing had used Explosion in the middle of the Kecleon shop, hurting the shopkeeper (the sprite flickered) and destroying all but two tiles and a stack of Gravelrocks. The Lanturn (under AI control) defeated the Weezing. Then the Kecleon followed the Lanturn around for the rest of that floor.
I never ran into any more enemies, so I didn't see if it would attack with us. It was rather neat.