Pregnancy Paranoia

Hi

So this is probably going to be a stupid question, but I'm in a long distance relationship, my girlfriend and I have been together for a little over a year now and are planning on moving in within a few months. Of course, until then, we have to make do with short visits every month or two until I have enough saved to make the move over there.
And of course, being a young couple (I'm 21 and she's 20) that only gets to see each other once every so often, we make up for lost time if you catch my meaning.

We're always really safe, she's on the pill and has been for a long time now, and I always use condoms. However, the last time we saw each other (which was on new years) we had sex, and halfway through we stopped as I realised that the condom had actually broken. I didn't ejaculate but there was some precum.

I know that the pill is basically 99% effective as long as its used right, however, my girlfriend is now late for her period, and she's basically panicking. She was expecting it about three days ago and is adamant that she's never late and she basically doesn't even feel the signs of having a period (she normally gets them really bad).

Should this be cause for panic and alarm or could a late period be brought on by something else? And what are the chances really of pregnancy in this situation? She takes the pill everyday without fail, however she has told me she doesn't always take it at exactly the same time each day. Not sure if that would make a difference in its effectiveness.

This is probably a stupid question anyway but she's really worried about it and its starting to make me worry too. Any advice would be greatly appreciated!