Yes. Dual nationals like myself cause problems with any other system. This time last year I left the UK with Qantas who weren't interested in my UK passport and didn't even open it as I wasn't entitled to enter Australia on it. So I flew on my Australian passport. Coming back I had to use my UK passport to get into the UK, so I did the trip on that.

Any attempt to track people in and out would require a major upgrade to airlines systems so they can hold multiple passports in the advance passenger information, or for immigration/emmigration to see all of a travellers passports. The problem then becomes what if I lose one and it gets replaced while abroad? What if I go abroad for a while and get one of my other passports renewed, the passport numbers now don't match and the UK has no record of what number replaced what. Assuming that name, DOB and place of birth are unique is wrong. Without an update to the global passport system tracking people in and out just won't work unless you give everyone who isn't a citizen an arrivals card with a stub to return on exit and check all citizens passports on exit and entry. Even then people forget the arrivals card stubs, I almost did in Canada this summer as I entered on my Australian passport and left on my UK one.