War and coups (maybe relations with India somehow becomes sour and they go to war over Kashmir rather than the peaceful solution that was reached IOTL). Pakistan post partition was very stable and had stable governance. Also becoming close with their neighbours india really meant that they could rely on each other for consistent trade so if they don't have that and have constant coups, warring with india and maybe even civil unrest and you have a possible recipe for disaster.
I also think Pakistan's secularism has been key to their success, despite being a muslim majority country, unlike Iran or the middle eastern countries, they haven't really let religion define their policies and that's probably helped them. So if you saw some kind of islamic sect rise there in the 50's or 60's, that could lead to destabilisation.