Although few will have published before starting a PhD, it is rare. An MSc is generally a taught degree, which has varying amounts of research involved, and so publications are not expected. Just having one publication will look brilliant for when you apply, but having relevent exoerience will also look good, so don't worry about it.
Yeah, it's quite rare to publish doing your masters. Although, having said that, it depends on your area. To publish in mathematics, my area, you'd have to be an evil genius. Okay, not necessarily evil. But fear not Sam, go out and apply !
I had one publication in NAR when I applied- but this is not that unusuall, because I spent 9 months full time in the lab (with no lectures) to obtain my Diploma (which is like a MPhil). As I was the only person who applied for the two PhDs on offer I don't think that my publication was an advantage ....