It was a stupid decision to leave out the boys. I mean hindsight is 20/20, but if heterosexual women were getting cervical cancer from HPV, and HPV is spread by sexual activity, then vaccinating the boys along with the girls would have been the logical thing to do in order to stop the spread.
I assume this wasn't done because they didn't do any studies on boys at first, because they were looking for cervical abnormalities to gauge vaccine effectiveness, and maybe it would have been hard to recruit a bunch of boys for a vaccine study that would probably not benefit them.
With that same hindsight we now know that HPV vaccination also prevents some oral cancers, and that leaving out the boys was a very stupid decision indeed.
These days most places do seem to also vaccinate boys. I got an HPV vaccine at some point in my 30s, and I pretty much had to wrestle my doctor into submission in order to get a prescription.