These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Brilliance: In the beginning of the movie (40 years from the present), the poacher that was hunting down Celebi had a Scyther. Guess what Dark Celebi's monster looks like?
Related to above, Scyther wasn't random. Neither was Houndoom. Both their dual types are at the very least resistant to Celebi's attacks, and both are strong against Celebi's own dual types.
While traveling with Ash and co., the viewers see that Sammy has a passion for keeping track of all the different Pokémon he encounters in his sketchbook, and once they realize that Sammy is Prof. Oak, it finally makes sense where the idea for the invention of the Pokédex came from.
Fridge Logic: If the Masked Marauder's Pokemon become evil, why do they continue to faithfully follow his orders? Wouldn't evil Pokemon be constantly rebelling?
Writer Cop Out: Some people might see the emergence of dozens of time-traveling Celebi to revive the main Celebi as this, especially since the film, for some reason, faked the audience out once with a previous Deus ex Machina that turned out to not do any good.