I just uploaded version 1.3.2 which ... reduces this error.
So the error shouldn't have happened, but unfortunately, the error occurred in a code-path that was already working towards showing another failure. Basically it failed to show a nice message and therefor showed fuzzy error instead! XD
P.U.M.P. isn't the smartest tool; it'll plan a layout for all the pipes above ground, and once everything is connected, it'll try to bury some parts of the pipes. In the save you provided the error that should've shown was that it can't perform a layout due to an obstruction; in your case, the rails.
The nice failure message is now properly shown. Which I guess is some sort of fix? It will have to do for now. Changing the logic of P.U.M.P. to be able to handle obstruction scenarios is not something on my TO-DO list for the immediate future.