I just discovered Upverter 5 minutes ago, and already found issues.
It is not hard to end up with something like this.
Notice the dots.
https://upverter.com/eda/#designId=d9f831c607b3e698,tool=schematic
if that matters.
I see what is happening with your design. When you draw your nets, the more you let the tool decide the initial path of the net, the less of this you see. The auto-router treats any point on the wire where the user has clicked as static. Dragging symbols around won’t move these points. Any point it placed itself is dynamic. Drag the symbol around and it will adjust the path accordingly. Junctions are therefore static because you had to have clicked there. The fewer fixed points on a net, the less likely you are to run into these issues.
the 3-way junction between R1 and C1 is actually at the dot. the wire leading to R1 is overlapping the wire to C1. If you were to drag the horizontal wire to the left upward, it should resolve the apparent misplacing of the junction.
The junction between C1 and GND is not a junction, but it is where the net overlaps itself. This is likely where you clicked while drawing the net. Then when you moved C1 around, it created the conflict.
I noticed that you have the schematic constraints turned off in the screenshot. When they are on, red indicators will appear over these regions. You can often just click and drag these highlighted regions to clean up the schematic.
That can be all true, but the schematic doesn’t give me the feedback that some nodes of nets are locked because I moved them.
I still consider this a bug. Explained bug is still a bug 
I would argue that, by not moving sections of a net when you move a symbol is perfectly valid feedback that its position is fixed.
I’m not sure if I would want this behavior to change. In my more complex schematics, if I can’t force a wire to stay where I put it, then the schematic starts to get unreadable as I move things around.
There is a balance to be found here, and IMHO, I think Upverter is close; Closer than some enterprise tools.