No they did not. They are saying they used the energy Alain collected to help control Zygarde not boost Charizard X.
Case closed.
Wow, that wasn't said at all, all that was said was Alain was used to collect energy for Zygarde. Nothing more
How the energy was gathered and its affects on both Charizard and his opponent or why he needed to collect energy from so many different opponents instead of just re-using the mega users already in TF's employment have yet to be addressed. Until we get a clear statement that the energy sucking bracelet was in no way draining and weakening opponents and in no way giving Charizard a boost with the energy it was stealing it remains just as much a possibility as Charizard simply just being that powerful (or the until this arc ends with no more mentioning of the the energy collection antics).
Disliking the theory that TF interfered in Alains fights is one thing, but adding little bits to statements in an attempt to prove a point is another altogether
Based on past actions (and never daring to try something new) I'm leaning towards the writers simply never mentioning it again but a reveal that Charizard was indeed pumped up with stolen energy (minus whatever had been dropped off at TF) and now he not only doesn't have that boost, but they have to fight a Mega Gyarados with ALL the mega energy Alain had gathered (making him by far the strongest and biggest threat imaginable) could lead to an epic battle and would be a great end to the whole Mega's and Ash-Greninja story.
Given that Ash was quick to forgive Alain and break him out of his funk, I seriously doubt he will be disqualified.
Ash isn't exactly the authority figure who decides that though.
Though even then I'm still waiting for anyone who wants him disqualified for unknowingly aiding TF to come up with a reason as to WHY that should disqualify him. If he won the tournament fairly, then what he does afterwards should have no bearing on his accomplishment. That said, does anyone besides Ash even know he aided TF because :S. Lysandre only broadcasted images of himself and Zygarde and he and Alain are standing at the top of the tower pretty much out of view. So unless he or Ash tells the general population, nobody should be aware of his (unwitting) involvement.
The ONLY acceptable way for Alain to lose the trophy is because the match was deemed tainted and a rematch required. Anything else is nothing more then a pity trophy and still means Ash came in second, not first.