Nibal,
If you are checking the option "Entire Palette" when running the schedule then you will see all equipment that is added to your project, including the items not placed.

If this is the case, uncheck that option and you will be good to run a new schedule. If you have not checked this option and things are still showing up incorrectly, use the Tech Support system to send us your files in question and we can help point you in the right direction.