I don't know that software, but I assume that the green arrows are the currents. And since the sum of all currents in a junction is zero (Kirchhoff's laws), and the green arrows both point away from the switch, one has to be negative. Or in other words, the direction of the green arrow at the battery is the wong way around. But when you consider the "wrong" direction and the negative current, everything is perfectly fine. I hope this isn't too confusing.