How should a PoE flyback transformer look on the oscilloscope

Measure at the pin not connected to the 48VDC line i.e. the pin of the transformer connected to the MOSFET / integrated flyback regulator IC (If unsure, try it out).

Depending on how exactly the IC works and the load (and the circuitry), these waveforms look quite differently. So the following pictures are mostly for basic reference.