Most of the time I see this error in Google Analytics two things are happening:
The Adwords Ad is targeting a page that has some sort of redirect
The redirect strips out the gclid parameter and Google Analytics records the session against the Organic channel.
If the site has recently moved from http to https check that the Ad destinations have been updated to the new URL.
In short you need to avoid sending traffic to any page that redirects. Strictly speaking redirects should not mess up tracking but I’ve lost count of how many time redirects are a part of a tracking problem.
There’s a couple of tools that can help here:
Check for redirects with: Redirect Path
Crawl the site with Screaming Frog and match the data up with the Ad destination URLS. If any of the Ad destination URLs redirect then update the destination URL in Adwords.
If you’re working on a site with thousands of pages then switch Screaming Frog for Deep Crawl which is web-based and handles large volumes better in my experience.
More info from Google Analytics help: https://support.google.com/analytics/answer/1034383?hl=en
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