That has to do with the tab setting in the TOC style and the settings in your MultiLevel Numbering List.
There is likely a left tab set where the errant page number is showing up. If you remove the tab stop it will give you the dot leader and right alignment.
Note where the text ends on the entries that show the problem.
Here is a temporary link to your sample document repaired.
Steps I took:
- I used the Define MultiLevel List dialog for your numbering in the document to change the character following your numbering from a tab to a space.
- I changed the tab settings for your TOC styles to have a right tab outside the right indent. Yours had it at 5.69" and I set it for 6 inches. This was done using the Tabs dialog, not the ruler.
- I changed the paragraph settings for TOC 3 to have a hanging indent. This was done using the Paragraph Format dialog.
I would suggest that you make a copy of your document and try importing the following styles from my repaired document into your copy and see if that helps:
Use the Organizer to import the styles. (The link is to my page on Styles.)