NOINDEX is a PAGE TAG
: if a page has a noindex meta-tag, Google and other bots that obey the tag - not all do - won't index it.
NOFOLLOW is both a PAGE TAG
and and a LINK ATTRIBUTE
: if a page has the NOFOLLOW tag (<META NAME="ROBOTS" CONTENT="NOFOLLOW">), Google won't follow links on that page; if a link has the NOFOLLOW attribute (<a href="anypage.htm" rel="nofollow">) , Google will not follow that link. However, Google may still follow other links to the target page that don't have the NOFOLLOW attribute, so NOFOLLOW doesn't guarantee that a page won't be crawled, and has no effect on whether it is indexed.
Use NOFOLLOW in the HEAD section of a page when you don't want Google (or other robots) to follow any of the links on that page. Use NOFOLLOW as a link attibute on any individual link you don't want Google to follow.
Use NOINDEX (<META NAME="ROBOTS" CONTENT="NOINDEX">) in the HEAD section of a page you don't want indexed.
Your decisions about which tags/attributes to use where on your own site should be informed by what you want bots to do (or not to do), not by any SEO objectives.
NOINDEX in the page HEAD will prevent that page from being indexed, so if you want that page indexed, don't use it.
Screaming Frog is only spidering internal links. If all internal links to a page have the nofollow attribute then it probably won't get crawled by Google unless there are third-party links to it.
Noindex will have no effect on links, as it isn't a valid link attribute. If you want pages indexed and crawled, ensure you have at least one internal link to them without the nofollow attribute, and do not use noindex on them.
[edited by: Wilburforce at 10:31 pm (utc) on Jun 10, 2019]