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Syrupy apples can be bought at Poppi Town on Wednesdays, Fridays, and Sundays. You can also buy them any day in Mirable City during the 4 o'clock festival (runs every day from 4-8 PM; interacting enough with Clementine gives you an option to extend the festival if needed) or anytime from the Thestal Jeweler.

The game does use soft exp capping to reduce the amount of exp that overleveled Pokemon receive, to try and even out your team's levels, though the case you describe sounds like it's just a difference of the exp group; Applin is in the group that takes the most amount of exp to reach level 100.

The goal is for chapter 4 to come out this year, though I can't guarantee that I'll be able to make that goal.