Sub-pixel sampling. Read up on it. you are placing your images at odd values and it gets resampled. Can be anything from the image inside the frame, the image frame itself, some styling option in ID...
Does your logo have type and/or vector elements? If so, save as a Photoshop PDF, then place into InDesign. Turn on overprint preview in InDesign (View> Overprint Preview) for a more acurate preview.