hi mavigogun,
you're right the little yellow dot on a white background, eye burn aside, is not a great color choice.
So I'm not at all defending the current state of the experience (it is being worked on and real world examples like this are helpful to us getting a better solution), just trying to provide a little nuance and clarity to James' scenario.
In this particular case there were a number of points and open points right on top of one another, which we don't do a great job of rendering in the graphics window to show and the pick list is long and lacks any information to diagnose the problem. I only found it by zooming in and tumbling to get the errant point to reveal itself, using the depth selector to cross highlight was not too helpful in this particular scenario.
as you can see, there are a lot of points stacked here, ideally the list should give some indication of the problem one, but today for resolving this problem it's not too helpful.

in this orientation I can't see the yellow dot, the projected reference that has gone missing

If i tumble just a bit, I see some indication of where the problem lies (small yellow point on top of: black points, several white points, couple green points; I counted 14 points stacked there) if I go back to the depth selector I still can't determine the which point it is. So at this point (no pun intended) I take the sledge hammer approach and drag select from left to right in that area and delete any free points, finish the sketch and the warning state clears, but the adjacent construction line is no longe constrained. (see previous post).

Again, I'm not defending the current experience and as the team is working on fixing it, anybody that would like to share similar scenarios with us will be very helpful in testing out our solution.
hope this helps,
Jamie Gilchrist
Senior Principal Experience Designer