My USB D+ and D- signals have what looks like a clock signal embedded onto it. The chip is a ISP1362
Could be these things:
1) The scope does not have enough bandwidth to capture the signal, get a better scope. (or turn up the time resolution if possible).  Make sure the probes can handle the bandwith also
2) The scope impedance is too high. Make sure the probe is clipped to the shortest possible distance between the signal that your monitoring and the nearest ground on the IC.