So, imagine if the Pokemon the bad guys used during this movie were all stolen. It's plausible, considering the fact that they control them using the Mega Wave thing anyways. Then, to add the cherry on top, any species they had that Ash also owns or owned, were Ash's and got stolen from Oak's Lab (Or Viridian Forest if you're Pidgeot).

Of course, this probably means that'd they fight extremely hard against the Mega Waves once Ash was in the picture, seeing a return to before in reach. Maybe they fight so hard they don't get controlled. Then they probably give their Pokeballs back to Ash. Maybe he would've only sent the Pokeballs over to Oak's lab until the end of the movie when they get sent back so Ash can continue in Kalos.

Since Team Rocket ended up with a Heracross (and a Pinsir but that's not important) they could've been like "huh, this Heracross seems familiar." and Heracross could've been using Team Rocket to find Ash after being handed over to them since he knows wherever Team Rocket is, Ash can't be that far away.