Some plugins use files that are called externally without beeing loaded by WordPress. By including some files from WordPress (wp-includes/plugin.php) is often among them they can then “load” up WordPress to do some WP-related stuff.
One example would be plugins that post some data from forms through their own files instead of the standard WordPress way.
I don’t want to vote for the strategy being good or not but I would at least have a closer look if possible or surf the Web for information if they are probably doing nasty stuff with that.