Change the Scaling options in the InDesign Preferences/.
Go to General Preference and change the "When scaling" option to Apply to content and then check.
BTW what's your OS ?
When you replace any graphic (including pdfs) into an existing frame of an Indesign document, the Crop to options must be identical from first import to replacing import for consistent scaling of art. If the Crop options are different, you will see this kind of scaling. Keep in mind that when you drag drop art into a document, the Crop to setting is the last setting that you have made. So if you placed art and changed the Crop to setting to "Bounding Box" any subsequent art placements will retain this setting.
After thinking about it, the size of the PDF might have changed, (the outside with the crop marks and info) since I am using a new PDF writer. thanks!