i had the same problem about three months into dating my boyfriend. that's how it started out was like a knife or cut inside as i was having intercourse, it turned into all around irritation and burning kind of during but mostly after sex, especially the first time urinating after sex. i've been into the dr's even an OBGYN and nothing has healed it completely. i stopped having sex even for a few months to "let it heal itself" and it's right back in the same problem. so i wish there was something to heal it if she has the same problem i have, but she may just not have enough lubricant. if you guys use lubricant make sure it's waterbased or it won't help the problem.otherwise, good luck!
If its a stabbing pain it could be an ovarian cyst. If she is irritated from the condoms, then she would feel "stingy" If its from the condoms I would take a break from sex for a little bit and let her body heal itself. Maybe she is allergic to latex or the spermacide. I hope it isn't a cyst but if it persists either way , she should go see her obgyn. Best of luck!