Hm. Let me see if I’m getting this…
You have various Media Sizes defined, and for one or more of these sizes — the thumbnails, it sounds like — you adjusted the crop area manually. So although all the image sizes are accurate, as defined in the Media Sizes, the standard crop area for some (which would normally be the center of the image) is different. And for some reason, when WordPress executed wp_generate_attachment_metadata()
it re-cropped those existing sizes.
Hm. If my description of the issue is accurate, then that is indeed an unexpected problem. Let me dig around wp_generate_attachment_metadata()
and see if I can avoid/bypass that behavior…
js.