When you build a rail line across a road you don't own, and it creates a crossing, then the way removal tool stops working. When you try to use it, either to remove the road or the rail line, it says "Ways not connected".
I have made a tiny savegame to demonstrate.
By the by, are we not supposed to be able to remove public roads anymore?
thank you for the report. Should be fixed in nightly revision 2944.