I do think you're confused. You say light B has wiring for 3-way, but
it doesn't sound like it to the rest of us- only one hot/black wire in
each cable. You say 3 cables enter box; sounds like these a 1
incoming power, 2 outgoing to light A, 3 outgoing to light B. The
dimmer ought to work if you connected as described, and also
reconnected those black wires you previously pulled apart. Is there
actually another switch which operates the lights?