It looks like you did not have a capital planet (as far as I can see on your Empire Tree) so maybe that's why it is set to -1. Still seems strange though.

Might be just a one off.

I think the problem is that the distance from the capital is determined by phase lanes, not by jumping through wormholes.  Because the planet that has the problem is between 2 wormholes that have no connection to anything else, the distance to the capital is not calculable, so -1 is just put in its place.  I could be wrong though.