This screencast doesn't share lots of information, too. Still would prefer the exported project. Here some guesses:
- Scroll back the timeline step by step and you will find the feature what created this point. Perhaps you get an idea how to delete this based on this information
- Left long click on the point.
- If it says "o" it's an origin:
- Right click -> "Find in browser" and you can find the related component.
- If it says "vertex" it's part of a geometry
- Right click -> "Find in browser" and you'll find the related body / component. Is it a linked component?
- Check your selection filter and ensure that "Select All" is and "Select Through" are enabled
But still - better answers do require an export of the project.