there really isn't any other way. You should buy a test and have her take the test. Evey women is differently, some women can "feel" pregnant, and have the sore breast, nausea, and backpain ect, and some women don't have anything. The dollar store has HPT, so if you guy don't want to spend alot of money just head to the dollar store. But if you guys don't do that, I would say to see a doc and find out why she didn't get her period. Sometimes when on birthcontrol women don't get their periods every month. There are alot of factors!
3 months is more than enough time for the BC pills to be doing their job. If she hasn't had a period this month, the only way to know for sure is to take a test...you could wait until her next cycle...but if she is pg, she shouldn't be taking the pill for the health of the baby.
I hope this helps and best of luck to you both!