Conflicting color spaces.
I suspect you have conflicting color spaces.
CMYK and RGB are color models, which are meaningless without a color space to define those colors. Examples of common color spaces are Adobe RGB, sRGB, FOGRA27/FOGRA39 (CMYK), SWAP 2 (CMYK) etc.
You need to make sure your InDesign document, placed images, transparancy blend space and export destination color spaces all match.
Document Color Profile
This applies to your Indesign Document and any placed images.
You can change the color profile of a document in two ways.
Edit → Assign Profile...
This changes the color space of the document but doesn't change any of the existing color values in the document. This may change the appearance of the colors as displayed on your monitor.
Convert to Profile
Edit → Convert to Profile...
(Only available in InDesign, Photoshop & Acrobat)
This changes the color space of the document and attempts to change any existing color values in the document to preserve the appearance of colors. This may still change the appearance of the colors as displayed on your monitor though.
Transparency Blend Space
Edit → Transparency Blend Space
In your InDesign document, make sure your Transparency blend space is set to the same color model as you document or intended output profile. You can choose from either Document RGB or Document CMYK.
PDF Color Profile
Assuming you have the correct color profiles setup on your document on any linked/placed files, when you export your PDF ensure No Color Conversion is selected in the export dialog (
Output → Color Conversion → No Color Conversion). If you do need to convert to another color profile, the best option is to change the color profile on your documents—but, as long as the color profiles are matching before hand you shouldn't have any problems.
Note: This assumes you are using Adobe products throughout your workflow and are using the InDesign 'Export...' to export your PDF. This is also all using CS6—The process may differ otherwise, but the concept is the same.