Ash's Lapras uses Sheer Cold, and no one bats an eye. Lapras can learn Sheer Cold, but it only learns the move at level 50 or above, hinting that it's older — and much stronger — than it looks.
Another subtle example also involving Lapras: Drake's Ditto transforms into them, and has no idea which move to use. This hints at Lapras actually being a disguised Mew, who can learn almost every move in existence. Transforming copies movesets in addition to appearance, which meant that Ditto suddenly had access to several hundred moves, and had no idea where to begin.
After being firmly established as a Kakashi expy, Grovyle happens to learn Grass Shuriken. "Lawn" in German is "rasen", meaning that from a certain point of view, he learned Rasenshuriken.
Aten becoming a Hisuian Zorua would be odd, until you realize that he was the ghost of a regular person - that is, a Normal Ghost.
Not only that, but it's said that Hisuian Zorua are reborn by their malice towards humans and Pokémon alike. A fitting Pokémon for someone who had hate and malice in spades to be reborn into.
Every time we've seen a Hisuian Pokemon has been due to either time travel or them being alive since long ago - the Wyrdeer was seen in an alternate timeline caused by Celebi, Celebi also later gave Professor Oak a Hisuian Growlithe, and Ho-Oh reincarnated the ancient king Aten into Hisuian Zorua.
Croagunk's appearance, being randomly added to Ash's pokemon in a Mind Screw fashion, seems odd until you realize his inspiration - of course a Sidereal's entrance to the story would be a Mind Screw!
Croagunk's bizarre reality-manipulation is just called "dodging". Why? Because Avoidance Katanote Parting Shot and Neighborhood Relocation Schemenote Court Change are both Dodge Charms!
While it can be written off as just an odd side effect of Ash being Ash, the horde of Dratinis he catches makes sense when you realize that Dragonite are pseudo-legendaries.
During his Lily of the Valley league battle against Ash, Paul manages to get Electivire to break out from being frozen by calling out to him. Now where have we seen that before?
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