Word limitation in journal paper
The wording here makes me think that the 6500 word count includes figures, tables, and references, as "to include" seems like a synonym for "including". However, it is always, always good to ask for clarification, especially when the wording, as in this case, leaves room for interpretation. I would email or otherwise contact the journal editor and ask for clarification. Contact information for the journal you linked in the comments can I believe be found here.