I have a website hosted at .github.io subdomain that gets 40 daily visits from Google search according to Google Analytics. When I'm trying to find out which keywords were used using Search Console, I see 0 clicks and just 21 impressions (most of which are for
(not set), which is fine) for the entire month.
For the other websites I host on my servers there is still a difference between Search Console and Google Analytics, but it's much lower, not more than 2x.
Does this happen because of being under a domain I don't own? Or it's a different problem?