This is intentional. AMP pages will always show up under the "Alternate page with proper canonical tag" list.  AMP pages are still able to be indexed, this does not affect their indexability. AMP pages simply use a special kind of indexing which is only for AMP pages, so Google doesn't show them as directly indexed.  Instead, they are "Excluded" but the ones that are indexed will show up in the "AMP" tab in Google Search Console.  Again, having AMP pages show up as "Alternate page with proper canonical tag" is intentional by Google, and does not affect their indexability.

Here is some more information from the Google Support forums regarding this: https://support.google.com/webmasters/thread/51692881