You're reading with the injectors hooked up, correct? The signals come from the ECU. The ECU grounds the injectors, completing the circuit. The pulse-widths depend on how much fuel is necessary; you can look at the fuel maps for this. Putting a oscilloscope on a injector is like putting it on a lightbulb; it'll only show how fast you're flicking that on/off switch.
A "bad" injector would have some issue with the electrical resistance; which means you would just check for resistance(which is supposed to be 12-15ohm).
The only time people use oscilloscope on injectors is to measure injector lag time at different fuel pressures and different voltages.
What exact codes is it giving you? Sometimes, the solution is something different; follow Honda's flowchart(in the Helms manual) to solve the issue.