You posted your question to the Edge Inspect forum. I've moved it to the InDesign forum where you have a better chance of finding someone to help.
The answer is to not use Preview and to switch to Reader or Acrobat. Preview, quite simply is not very good with anything but plain vanilla PDFs.
Thank you Mark : )
I did solve the problem and it only occured on one document in which I changed the automatic bullet point color. I usually make my own bullet points, so this was a first for me.
Here is how I solved the problem:
When exporting the PDF, I chose the "Output" option and changed the "Color" to "Convert to Destination (Preserve Numbers)". I then selected "Color Match RGB".
This worked for the problem document and it didn't happen again on other documents.