If you have created a report and are not seeing the desired results, this is likely due to one of the report filters. To troubleshoot this repeat the following steps for all the filters you have on your report.
In this example I will use Opportunities but it will work for all modules
On the Opportunities module, click on the blue Create button
Select the filter and add in the criteria here
Click on the + button to add a new filter
Repeat these three steps, until you lose all the results from the list view. This will show which filter is causing records not to show.
Field is empty filter not showing results
If you are running a report which filters on something not being empty that doesn't return results when you believe it should, edit the filter to say "Is not one of" and highlight all the options.
If this fixes your issue it is likely that these records are appearing blank due to a deleted dropdown option.
Duplication within a report
This is almost always caused by filtering on a related module where the duplicates have multiple related records in that module. For example a common one is an accounts report is showing the same accounts multiple times, and is caused by filtering on related addresses. An account with 3 addresses would show up in the report 3 times.