I lived in Puerto Vallarta for 5 months last year in that same area, and never had any untoward experiences with either local citizens or local police. I walked around that area almost every night in the late evenings and occasionally the wee hours of the morning.
PV is not a perfect place, but the crime there consists mostly of very occasional pickpocketing or petty jewelry theft. The police by and large are good people, although one hears of the very occasional not-so-subtle traffic stop - I guess that can happen anywhere in Mexico. There are ways to act to lessen the chance of paying the mordida.
It would be very frustrating to have been stopped like you were. However, it was a brief incident, and really no extortion even attempted. I suspect because you and your friend could not communicate with the police well, and perhaps started to get in the truck, they may have interpreted it as pretty strange behavior, and frisked you.
Frustrating and a little frightening, yes. An international incident -no. I hope you had a nice time the rest of the week.