This is most commonly caused by setting a bleed in your InDesign file. In order to use a bleed with the InDesign plugin, you will need to create your master pdf to be the size of the finished product plus the bleed. For example, if the finished product should be 5" x 5" and you want an .125" bleed, then your master pdf needs to be 5.25" x 5.25". Remove all bleed settings in InDesign. You can then set the bleed on the Template Info tab of the template in eDocBuilder.
This can also happen if you have bleed settings in your export to PDF settings in InDesign. The plugin makes use of the PDF export settings in InDesign. It will use the settings from the last time you exported to a PDF from InDesign. Make sure that your PDF export settings do not include any bleed settings.