I remember my teen sims used to age up when they called to enroll in university, now they moved into the university neighborhood but they are still teens, does anyone know what may be causing this?

I believe you might be thinking of TS2 there if you ever played that version of the game. Enrolling in Uni has nothing to do with aging up in TS3. Under EA standard, only those who are already YAs and older may attend Uni, teens have to wait until after their birthday age-up to YA though I believe they can take the entrance (scholarship) exam early if they like. NRaas Traveler by option unlocks teen registration in Uni, but once there sims will not age anywhere in the game as time is frozen just like in the WA and other vacation worlds.

Is/was your teen unable to age up when they were back home, either by reaching the end of their defined teen life span or by being presented with a birthday cake and directed to blow out the candles?

They were able to age, but I saw the option to enroll there so I thought they would age up by going there.
I guess I will need to reload my save and make them age up first

Either that or play though with them being teens at Uni to see what that feels like and then they can age up once back home (and then attend high school graduation if you wish, admittedly that part runs a bit backwards). I mean, I was a teen when I started Uni, I was still 17 in fact. It wasn't really more of an earth shattering experience than for those who were a bit older at the time. Although if you play with restrictions in place on things like teen romance I suppose that could make things a bit different that first term than they otherwise might be.