When plots and subplots can't seem to match up, it may be you need to eliminate a character. By this I do not necessarily mean the character will die in the story, although that is certainly a possibility. No, rather, have your extra or unnecessary character go on an extended vacation, or have him or her tangle with a problem that takes him or her miles from where the rest of the story starts to happen. Or, you can simply rewrite it without him or her and see if it makes a difference. Having more characters than we really need means that each of those characters needs to be fleshed out and attended so as not to appear hollow. Or unneeded.