Yes I have also had partially routed boards via auto routing behave the same way
Sometimes it also depends on the schematic.
I have found that if I have say a GND connector then I connect a component to it ( lets say a resistor), and then I make another connection to another component to the same GND connection, depending on WHERE I connect it and the resulting net name, dictates how the rats nets behaves.
So sometimes B1+A1=GND is not the same as B1=GND !!!!!, even if I route the COPPER directly from B1=GND , you have to BACK annotate the copper to the schematic!!!
Sometimes on the schematic you have to specifically draw A1=GND, B1=GND ( actually when you think about it, you might want a connection to be made a specific way , not always the 'common' sense way, for example you may want to specifically route a ground plane connection to a given point even though there is an 'equivalent' (as in multimeter, not signal) point near by.