The confusion comes from Vakama knowing it's Makuta. When he sees Dume he thinks back to the false Turaga asking him for the Mask of Time, which morphs into Makuta's voice.
Vakama then tells Onewa that he doesn't want to know who's in charge of Metu-Nui. This wording, combined with the Makuta voice from earlier, implies that Vakama very much knows Makuta is in control and that this is a very bad thing.
That in and of itself isn't a plot hole. Of course anyone being in control of Metru-Nui other than Dume is a bad thing, but the confusion comes from why Vakama reacts with conviction and certainty instead of how Lihkan reacts: with sheer surprise.
I realize that there may not be a plot hole in actuality, and yes, the movie is pandering to what the fanbase knew at the time (that Makuta is and always was evil), but it's the wording and the tone that leads me to see it as such.
In summary, Vakama's reaction is in conflict with the appropriate reaction seen a scene later from a much more credible character.