What you experienced is the result of the "Ignore path part in URL (domain only)" option being enabled in your settings. When that option is on, the extension considers any two tabs on the same domain as duplicates, regardless of the path. It is off by default.

Turning that option off in the Options page will restore the default behavior, where only tabs with identical URLs are considered duplicates.

If you are still using the extension, v4.2.0 was just released with a number of UI improvements, including a clearer duplicate tabs list that shows which tabs will be closed.