I'm not sure what it is I am doing wrong but I seem to lose junctions in eeschema. This has happened 5 or 6 times in the project I'm currently working on and happened again just now. I was tweaking my layout and went back and forth between eeschema and pcbnew a couple of times. When I ran DRC (which I do frequently) it complained of an overlapping problem. I notices that the errant trace ended in a via to "nowhere". Looking at the schematic, the pin had lost it's junction. It wasn't that way 10 minutes earlier.
I had added a resistor and placed/routed it but then changed my mind and deleted it. Some how this lead to the lost junction. Is this a known problem? The resistor did not connect to the lost junction and wasn't even on the same schematic sheet.