I know this is a really old post but I had this issue and just figured out how to get rid of the Red Dot.
Step 1: Tap the red dot and tap the Save to...
Step 2: Tap New Guide...
Step 3: Name the location whatever (it's about to be deleted)
Step 4: Name the Guide (again, will be deleted)
Step 5: X out of the location and swipe up on the Maps control screen. Below Favorites you will see My Guides. Swipe your new guide to the right and delete it.
If you have multiple dots with this, you can actually add them all to this and delete in one action. Hope this helps.