Started having this problem since last updated, Webstorm 2017.2.4
Debug a NodeJS project (Node 0.10.48), where I place a break point before starting. Breakpoint is hit and all is fine. However, if I delete the breakpoint within the debug session, it keeps stopping at that point. I've opened the breakpoint window and force deleted everything. Still stops at my old line.
When I stop and restart the debug session, everything is fine.