[Taqwus]

It's a wild shot in the dark, but this might occur if they're using integer arithmetic to update populations and an overflow happens.
e.g. instead of

x += x * (pop_growth/1000.0) with floating-point arithmetic, using
x += (x * pop_growth) / 1000 with integer arithmetic.
If x*pop_growth or similar expression exceeds approximately 4.2 billion (unsigned 32-bit integer) or 2.1 billion (signed 32-bit integer) weirdness could happen... although landing at exactly zero is strange unless there's a follow-up check that sets x to 0 if it were otherwise negative.