This is very tough without actually getting under the hood in GSC. Based on your comment it also seems like the problem got resolved, but I'll list some possibilities to consider for anyone that finds this in the future.
Mixed Methods of Specifying a Canonical
There are a variety of ways the canonical can be set. Mixing these methods could cause an issue like this.
rel="canonical" HTML annotation:
<link rel="canonical" href="https://example.com/" />
rel="canonical" HTTP header:
Link: <http://www.example.com/>; rel="canonical"
All pages listed in a sitemap are suggested as canonicals; Googlebot will decide which pages (if any) pages are duplicates, based on similarity of content.
Canonical Guidelines (via Google Webmasters)
Don't use the robots.txt file for canonicalization purposes.
Don't use the URL removal tool for canonicalization. It removes all versions of a URL from Search.
Don't specify different URLs as canonical for the same page using the same or different canonicalization techniques (for example, don't specify one URL in a sitemap but a different URL for that same page using rel="canonical").
Don't use noindex as a means to prevent selection of a canonical page. This directive is intended to exclude the page from the index, not to manage the choice of a canonical page.
Specify a canonical page when using hreflang tags. Specify a canonical page in same language, or the best possible substitute language if a canonical doesn't exist for the same language.
Link to the canonical URL rather than a duplicate URL, when linking within your site. Linking consistently to the URL that you consider to be canonical helps Google understand your preference.
Google recommends checking for the following if you experience unexpected behavior:
- Incorrectly marked language variants
- Incorrect canonical tags
- Misconfigured servers
- Malicious hacking
- A copycat website
Details on these can be found here
Multiple Search Console Properties
I've seen anomalies like this occur when a site has other unknown or forgotten about search console properties. There are two types of properties:
- URL-prefix property
- Domain property
See this page for more info on both.
Search Console data is scoped into each property. The property that gets the data, depends on what is indexed, ranking & getting clicks in Google search. What is ranking really depends on your domain/redirect config.
Make sure that you're using the Domain property and that there are no older properties for specific URLs such as