In the Explorers games, the player can receive Eggs as rewards for missions or randomly in Spinda's Juice Café. These Eggs can be hatched in Chansey's Day Care, and you can then have them join your team. But these Eggs are unborn Pokémon, often of a species unrelated to the clients giving them out. Where did they get these Eggs? And why are they accepted as payment in exchange for rescue/bounty hunting services?! And why did that strange Pokémon at the bar just give you one based on watching you drink?!
When the player apprehends an outlaw, if the reward is monetary, Magnezone calls it "the bounty on this outlaw's head." Does that mean that the outlaws are executed after capture?
That phrase can refer to someone captured alive.
Does the ending of Pokemon Mystery Dungeon 1 remind anyone of Suicide?
The hero used to be a human. Assuming this, he or she would have friends and family... in the end, he or she stays as a Pokémon, so what can the friends and family assume? Their child would be a missing person... or worse, dead.
I was never sure how Team Skull got their name until now. It's because they're all Poison types, and a skull and crossbones is a common symbol for something being poisonous. Also, that same marking is on Koffing's body, so it could have been named in honor of him as well.
Chapter 3 of the Explorer games is called "The Scream." Playing the game through the first time, the player assumes this refers to Azurill's scream, which you hear in your first vision. However, you learn later that your visions are called Dimensional Screams.
There's a good reason why the heroes had to fight Primal Dialga in the second game first: if they showed who the game's real villain is early on, then the game would be shorter.