Paula, this is one of the drawbacks of charging by the word; with a project fee, you can add in the fudge factor, plus other incidentals like follow-up emails and so on.
For CE, I don’t remember typically having a lot of follow-up conversations with the author, so I didn’t usually worry too much about responding to one or two emails–that was just part of “overhead.” For DE clients, I add an hour or two of coaching calls into the project quote because typically the client will have some questions about how to approach the revision or will want to brainstorm.
My project quote does limit what the edit includes; I don’t do meetings as a typical part of an edit and would charge if I did, including accounting for travel time, etc. I try to make it clear that the edit is the edit; people can pay a coaching fee for phone calls, meetings, etc.
If you’re going to charge by the word, really the only thing you can do is make sure the per-word rate covers these issues–that is, that you not only are fairly compensated for the edit but for the ancillary issues around it. It can be a race to the bottom, though. There’s always someone who can do it cheaper than you can. So I encourage people to find ways to quote project rates or at least to minimize scope creep (“Can we have a quick call?” “My fee for quick calls is . . . .”)