The Pokémon Adventures manga series does sometimes include the other trainers and puzzles in the gyms. In Pokémon Adventures: Diamond and Pearl Platinum, Lady Berlitz usually does battle the other gym trainers and complete the puzzles of the gym, however it is usually glossed over. Instead, the manga usually focuses on Diamond and Pearl as they try to catch a glimpse of Lady's progress since they are barred from entering the earlier gyms. For instance, in volume 2, Lady Berlitz visits Gardenia's gym. On page 13, the guard statue explains that Lady Berlitz has to defeat four trainers hidden in the forest maze and then make her way to Gardenia. On page 15, after getting kicked out of the gym, Diamond and Pearl find a window to watch the gym challenge and discover that Lady has already reached Gardenia:
It's amazing, Pearl! Lady got through the maze already and beat all of the preliminary trainers! She's already facing Gardenia!
-Diamond, Pokémon Adventures: Diamond and Pearl Platinum Volume 2, pages 14-15
Some later gym puzzles, such as the math problems in Fantina's gym, were shown more explicitly.
Likewise, in the Black and White chapter, gym puzzles were shown. At the first gym, the puzzle was to step on a switch representing the Pokémon type that was effective against the Pokémon type on a series of curtains. When Bianca interrupted Black's gym challenge by stepping on an incorrect button, the three gym leaders agreed to a three-on-three battle if Cheren and Black helped her out and the three of them made it through the curtains.