I'm think it was most likely rust that had formed on the rotor, which increased friction for the first or second application. Now if it doesn't go away, then I would have some concern.
It is certainly worth trying to keep your chemical products off the rotor, pads and calipers. Not so much the chemicals themselves that are the problem, IMO, but the grime and oils that can be released and settle on the pads and rotors. Those surfaces really should stay free of contamination for best braking performance, though I doubt it will actually affect noticeable change in practice. If there is concern, such as on a high-performance car, I'd recommend following a brake pad bed-in procedure to restore performance. For a normal car that is just driven around town, especially with an automatic where you tend to coast with the brakes frequently, it probably wouldn't hurt either, to heat up the pads and clean off the rotors. But if you can't safely bed-in the pads (can't have cars behind you!) and drive for a distance to let them cool off without stopping, don't bother.