Regenerating thumbnails warps new Site Icon in some scenarios

The plugin will regenerate thumbnails that shouldn’t be regenerated, in the case of the new site icon feature.

Recreate:
0) Set WordPress’s “thumbnail” image size to a non square value, like 300×200.
1) Upload a square image or at least something greater than 500px by 500px into the Site Icon feature of the customizer.
2) Notice the square site icon, as expected (see favicon for sample, or source code)

Output is as follows:

<link rel="icon" href="https://local.wordpress.dev/wp-content/uploads/2015/10/cropped-site-icon11-32x32.png" sizes="32x32" />
<link rel="icon" href="https://local.wordpress.dev/wp-content/uploads/2015/10/cropped-site-icon11-192x192.png" sizes="192x192" />
<link rel="apple-touch-icon-precomposed" href="https://local.wordpress.dev/wp-content/uploads/2015/10/cropped-site-icon11-180x180.png">
<meta name="msapplication-TileImage" content="https://local.wordpress.dev/wp-content/uploads/2015/10/cropped-site-icon11-270x270.png">

Now rebuild all thumbnails. Output is changed to this:

<link rel="icon" href="https://local.wordpress.dev/wp-content/uploads/2015/10/cropped-site-icon1-325x165.png" sizes="32x32" />
<link rel="icon" href="https://local.wordpress.dev/wp-content/uploads/2015/10/cropped-site-icon1-325x165.png" sizes="192x192" />
<link rel="apple-touch-icon-precomposed" href="https://local.wordpress.dev/wp-content/uploads/2015/10/cropped-site-icon1-325x165.png">

In my case, 325×165 is the thumbnail size. So all site icons are replaced by the thumbnail, when they shouldn’t be touched if they were uploaded for the Site Icon feature.

https://www.ads-software.com/plugins/ajax-thumbnail-rebuild/