All aircraft have weight variations. In fact I recall a comment from the bloke who was responsible for the 747-400 initial deliveries, to the effect that "all of them were the same, until we got OJB".
There are tolerances in everything. Whilst they might be pretty narrow in the more important engineering areas, they will be dramatically less so in items like cabin fittings. So, whilst there will be swings and roundabouts in what items weigh, the end result will never give you the same total weight...even variation in paint thickness will give a measurable result at the end.
The aircraft themselves have different equipment in them. Not just from orders with slightly different options, but the boxes themselves tend to vary as the makers find better or cheaper ways to make things.
And, in the case of the 380 in particular, the aircraft was always quite a bit heavier than what Airbus had wanted/promised, so there is an ongoing weight reduction process happening on the manufacturing line. Having said that, in service aircraft tend to get heavier with time.
Car manufacturers have this sort of thing down to a fine art, but I'll bet that if you take two ostensibly identical cars and weigh them, there will be some level of variation...and they get to make millions of the things, not a paltry few hundred like the aircraft makers.