How to measure a clock signal from a positioning module with an oscilloscope
It depends on how frequent the missing pulses are present in the simulation and what oscilloscope you are using. If the missing pulses are frequent you should be able to detect them on your oscilloscope. If your oscilloscope is a digital storage one, you can set it to sample for a long period, you can then slowly investigate the capture manually to see the frequency. You can also try using math functions on your oscilloscope to detect the missing pulse; however, if the missing pulses are infrequent this will be tedious to do.

If you have access to a spectrum analyser that could also be potentially used to detect any anomalies in your clock signal. 

Depending on your background/expertise, you can also write some code on a microcontoller/fpga/etc.. which monitors the clock. You will specify the clock frequency expected, the code will sample the wave and increase a counter on every missed pulse. See the counter result and you will know if any pulses have been skipped.