Here is an image with the numbered 'incidents'.

1) I had a square around the center purple temple first, but as a I was attaching just the basic long, simple roads to the right, left, upper left etc., when I got to the last one (upper right), the square just disappeared on me - and then I redrew it as a circle and it seemed to stay. (not that I think the shape matters).
2) Similarly, I had the square around the large brown symbol first, then added the smaller roads to it and at some point the square disappeared. I redrew it which usually fixes the issue, but it's still odd.
3) On the opposite side of the issue, we have the brown pathways in this image. With the circled one, it suddenly added an additional random path off to the left, several centimeters from where I was clicking.
I think these might both be related to the same issue, something about saving what the user has done going haywire maybe.
Hopefully this helps.