I've run into the same problems everyone else has with some junctions and some segments refusing to be deleted. Hopefully things will be fixed soon, but I did discover a workaround for removing junctions (at least for the NA server).

I've mostly been removing excess junctions from one-way segments, and I what I've noticed is that the directionality of the segments attached to a junction must agree with the little 'A' and 'B' shown at a segment's endpoints when it is selected. In other words, the entrance of the segment must be A and the exit must be B. If a segment has A and B reversed then I get a server error. The workaround that has worked for me every time so far is to disconnect the exit point of the reversed, "B->A", segment from the junction and then reconnect it. The A and B should be switched (change zoom levels or you'll still see the previous cached result) and the junction can be removed. With two-way streets I've sometimes had to try multiple variations of disconnecting and reconnecting because I couldn't be certain which ends the A and B were supposed to be on.

Another workaround is to use the 'bridge' function, but it doesn't always succeed. When it works, the junction is still there but nothing is connected to it and it can be removed. Have to remember to set the level attribute afterwards, though, to keep them consistent.

Hope that helps.