Squeezing pairs, or sets of four spokes serves a different purpose than flexing the rim the way the OP did.

Rim flexing is about creating slack in some spokes to detect and/or correct spoke windup. However it's done, it's an important step, especially when building with thin section swaged spokes. Every skilled builder I know uses a variant of this technique, and the OP's bad luck doesn't invalidate the method. However, it's a reminder of the need to appreciate the risk, and exercise due care.