It sounds as the person at the counter measured it slightly differently than you did.  It often happens to me; say I am posting a box which I measure as 50.5cm x 30cm x 40cm.then the person at the counter measures it 50cm x 30cm x 40cm and it ends up bit cheaper than I quoted, as I always measure such a way that rather overestimate, it is rarely that I pay more than I quoted. 

No system will ever be perfect.  You have to allow for the human factor.  🙂