Site header is hogging my keywords?

I have a new Squarespace site I'm working on (and learning SEO as I go). I got my keywords for each page on my title, description and my single H1 tag, which all seem to work, more or less for a first attempt. The issue is that when I use site checkers (2 chrome extensions and like 4 different SEO checker sites) They all report really odd keywords that are either my header links (Home, portfolio, About, contact us) or "menu" which doesn't appear anywhere on my site at all that I can see. I can't see anyone having my issue online, so not sure if it's a squarespace or an SEO issue, but I want to know if I can request they not be scanned as keywords and have the rest of my SEO still work? and What is the best way to handle this issue? Top keywords from SEO scanner website: Portfolio - 4, Menu - 4, \[name of company\] - 4, home - 3, contact - 3 On a Chrome extension, my main intended keywords are the top 1-5, then after that are "portfolio" and "menu" -- again, menu does not appear visibly on the page at all.