Ref T12450. There's currently a bad behavior where inserting a document into one search service marks it as up to date everywhere.
This isn't nearly as obvious as it should be because bin/search index doesn't make it terribly clear when a document was skipped because the index version was already up to date.
When running bin/seach index without --force or --background, keep track of updated vs not-updated documents and print out some guidance. In other configurations, try to provide more help too.