Go to User Settings → "Miscellaneous" → "Show count of all replies ☑" to make it count the full reply-tree, rather than just immediate replies. As mentioned in Help for User Settings:

Show count of all replies: When viewing posts in sections or on The Monastery Gates, you will see the current number of replies. You can have it show you just the count of immediate replies ("children"), or the count of all replies ("descendants"). To get the latter, check this checkbox.