I guess you mean lissajous figures?
Lissajous figures are odd beasts. A phase difference of zero produces a diagonal line of 45 degrees.
Whether you did it accidentally or deliberately, it seems to me you would have to adjust CH 1 and CH2 to a matching proportion, to obtain X/Y plots which showed similar angles onscreen.
Did you verify at least a few of your readings, by doing a direct a comparison of the sinewaves, with one displayed above the other on a dual trace?