Exactly how many references to the movies have been made and what exactly were they in the anime? And I mean actually referencing them, not just because 'said' character didn't scan a legendary... it's not really proof of anything.
We had multiple references to the first Mewtwo movie in OS episodes
We saw TR witness the destruction of the TR base and Mewtwo fleeing in an main series episode
We saw Mewtwo in Armor multiple times in OS, and Gary even battled Mewtwo and got rocked
For Power of One we had James literally mention the same Lugia in the Johto arc involving Ritchie, Ash and another lugia and it's baby
For the Celebi movie, we saw Ash knowing what Suicune is in the anime when he never saw it before except as a silhouette and knowing it by name
For Destiny Deoxys, Drew's hometown in the main anime is the same as the location the movie was based on
For Jirachi wish maker, in the movie itself Misty is mentioned although that could be a dub addition
For the DP movie trilogy, Dawn has the Lunar wing from the movies she brought with her
For Genesect legend awakened, we see N in the main series seeing the Genesect designs and seeing the Genesect army from the movies fleeing a TP base