Hi, tyeago,
Here are two recent threads where other users have reported
similar problems:
"Multiple/broken/repeated
listings in Search results"
"Double-entry
Search results!"
So, the proposed solutions are:
1) Make a backup of your project. Then rename the .cpd file
and reenter your project.
2) Try creating a new single source layout.
3) Check the hyperlinks in your topics for any that
inadvertently point to target topics that are above the root folder
of the help project.
Pete