Well, humans are weak and can be easily killed compared to Vampires and Lycans, however IPU had more numbers, training and military resources (tanks, drones, aircrafts). Immortals also have limitations: most Vampires can't fight in daylight and not all lycans can change to their wolf form at will.
Still too be able too train personel so fast too fight against infected witch are more powerful, plus in single purge they decimated Vampires and Lycans. Plus even with Selene finding that task force is after michael and warning him both selene and michael were captured without killing any IPU member not too mention intro scenes where it shows how IPU battles transformed Lycans and vampires.
Yes, it was very weird how easily Michael and Selene got captured, and also they never explain how IPU knew that they were both hybrids. but let's assume that vampires or lycans could been infiltrated some of the IPU ranks just like the lycans have infiltraded ANTIGEN without anyone knowing.