The repair of Little Chicago is a pretty major thing, implying a hidden character who did something for unknown reasons. I'd say it VERY unlikely that Butcher just wrote that in and thought, "Eh, I'll figure out who did that later."

The Calvin and Hobbes thing is a little different. It's possible it was just thrown in, but it's so... deliberate and out of place, and so "casual" that it seems likely Butcher has an explanation for that, too.

If you don't remember the scene, it's a little tense. Harry's just fought off an attack from unknown goat-monster things. He's bantering a little with Bob, but he has a broken nose and two black eyes and is a little worried. Suddenly... Calvin and Hobbes? Then Harry thinks to himself, "Hm, weird," and the plot moves on.

It wasn't put there as a joke- there would have been a different rhythm and tone to its mention. It wasn't mentioned by accident- Butcher deliberately typed those words.