There are many causes of bottle variation, some relating to the wine, some to its container. Before the advent of inexpensive stainless steel tanks, it was not customary to blend all the wine together and bottle it at once, a process called assemblage. Instead, the winemaker would simply take his or her siphon from barrel to barrel and fill the bottles from a single barrel at a time. Some traditional and/or idosyncratic wineries still do this, including Château Musar. Also, buyers and sellers of bulk wine typically do not have access to a multi-million gallon tank, and so often the wine will vary depending on which tank it came from.
Bottle variation that increases over time typically comes from the packaging. Exposure to heat or light can cause a wine to mature more quickly or even make it taste "cooked". Bottles aged in the chilly cellars of Sweden's alcohol monopoly are famous for tasting younger than the same wine stored at a more typical 55F. Finally, not all corks seal equally well, and a faulty cork will allow air into the bottle, oxidizing it prematurely. However, a corked wine would be described as a simple fault rather than bottle variation, even though the corked bottle would be clearly different than a non-corked example.
And sometimes, it is not clear what causes the variation. Bottles stored together their entire lives, with no obvious faults, can taste completely different. Thus there is a saying, "There are no great old wines, only great bottles."