Actually, I've seen a bug with Pioneers in the queue. If you have Pioneers in the queue and the population goes past the level-up mark, then you cancel the pioneers (not right away), the town will think it's already leveled up and will have the higher level, but it won't upgrade. I haven't reported it as a bug yet because I haven't been able to reproduce it reliably, so I can't provide exact steps, but that may be what's happened.