I tried to make a PCB having an Arduino Pro Mini on it. This has on the smaller side pins for the signals GND, VCC, RXI, TXO. However, these are usually not connected to the board, as they are used for programming. So, either those have pins connected on top or are not connected at all.
Note, that these signals are also available with pins on the larger side of the Pro Mini. When the Autorouter is run, it makes connections not only to VCC on the larger side, but also to the VCC on the smaller side, i.e. that for programming the Pro Mini.
I could overcome this situation by drawing a connection by hand. But is there maybe a way to stop the Autorouter making connections to certain pins?