During the middle of primary action in the film, a quick cutaway to the lab in which scientists are testing the element "Transformium" that is the metal all autobots and decepticons are made of, used to transform into anything, the main scientist is seen clearly holding a transformium-made Rainbow Dash for all to see. This wasn't subtle, but on-screen for about 3-4 seconds before dissolving/transforming into something else. The computer nearby, controlling the element shows an outline of Rainbow Dash with the words "My Little Pony" above it.
FatherofGray says: In case you are unaware, Toshinobu Matsumiya has been a key member of Game Freak's staff since the dawn of Ruby and Sapphire. He has participated in many roles with the Pokémon games since then, but has been the game scenario director in all of them. When asked how long the time gap between G/S/C/HG/SS and D/P/Pt to B/W is, he simply replied "Elapsed time is a secret. Imagine freely!"