I know it's a source of worry but I don't think the lack of a 6th capture by the "time" of the movie is a big deal. I think what we need to remember is that these movies are always very much saga-based. They don't seem to worry about the movies fitting correctly in the timeline between specific episodes anymore. (Not since the Mewtwo days, at least, but feel free to correct me) I mean, as we've seen in the past, evolutions have sometimes been wrong and captures have even been early (so the release dates are an especially unreliable indicator) So, I'd think that this specific movie is representing the XYZ arc. As in, the XYZ arc with the Zygarde and Team Flare shenanigans we're currently seeing.
I'd say that once Wulfric and the Flare plot are done, we'll get more details about what I'd call the "Kalos conclusion" arc, like the Kalos League, the 6th slot/Goodra return/whatever. I think a good indicator is the opening, which only covers up to the Wulfric and Zygarde parts. From a writing standpoint, I'd say it's a way to make sure that things don't slow down too much once it's time to start prepping for the League.