This does seem like a genuine problem, I had sudden population losses but then the population after an hour or two returned.
I also had a weird one whereby my carts 'died' whilst still in my towns and I got the population from that and had to build the carts again.
But I've also had inexplicable loss of troops (troops dying when they're not away on missions) which obviously gives me the population back, but is still annoying as it takes time to build the troops again.
I had an answer about the carts, but I've never seen an answer to the population 'bug' it would be good if a mod can clarify this for us.