This could arguably be considered a bug in my opinion. Media (any episode file, movie file, or video file) that is in more than one library, is shown with a duplicate in “Home → Continue Watching”. The only way to avoid this is to change the visibility option in [Library Edit] to “exclude from home screen” and/or “exclude from home screen and global search”. Choosing either of these options also restricts any custom collections (even if checked to display on Home" in Manage Recommendations from being displayed.
Please add an option to “Exclude from Continue Watching & Recently Added” that would avoid the files from being included in those two auto-generated/smart collections BUT would still allow custom collections that are marked to display on Home in [Manage Recommendations] to be displayed.