Hmmm, I can think of multiple different approaches that fit your description of this issue. Please post back with more details.
The simplest way to keep entries out of a typical FileMaker summary report is to keep those records out of the found set when you produce that report. But other options may also be valid approaches here depending on exactly what you have set up and what you are trying to do with your script.
Screen shots of your report in layout mode, screen shots of your script in the script editor (or copy/pasting it as text if you copy from a Database Design Report, a PDF of your script or via a third party developer tool) are welcome.