Google’s John Mueller answered a question in the Google Hangout from Tuesday on why sometimes you will see in the search appearance HTML improvements for duplicate titles and descriptions in the Google Search Console when those pages are using rel=canonical?
The question was asked at the 25:20 mark into the video:
Does a search appearance HTML improvements, duplicate titles, and descriptions in Search Console take into account the link rel canonical? We’re seeing it complaining on pages that have this added.
John Mueller said it may show temporarily but over time, it should settle down. He said:
So what’s probably happening there is that we’re indexing the pages with a rel canonical first as the version that we find it, because we have to kind of index that version in order to process the rel canonical. And then in a second step we’re actually following the rel canonical and using that to index the canonical version.
So what might happen, depending on the timing, is we have one version indexed like this and one version indeed like that. And that might show up as a duplicate in search appearance there.
In general though, that settles down fairly quickly in that we follow the rel canonical. We focus on canonical version and over time, you would see primarily the canonical version in these search features.
Here is the video embed at the start time: