First and simplest answer is that jacketed bullets and cast lead bullets are always sized slightly differently because of how the harder surface metal of a jacketed bullet grabs the rifling.
So you'll see that a jacketed bullet for a .45 ACP will measure 0.451" or so and a cast bullet for the same round will usually measure 0.452. The softer bare lead engraves more easily in the rifling and so can (and needs to) be a little larger in diameter to start with.
The difference is well pronounced for .44 Mag/Spc. bullets, where jacketed are always sold at 0.429" and cast are usually 0.431".
The next level answer is that guns actually measure all over the place for real groove diameter. Some are more consistent than others, but when you're trying to chase down a problem with a gun that tends to "lead up" a lot with cast bullets, you'll often find that the real groove diameter is several ten thousandths larger than you'd expect. And good manufacturers cover that problem by offering bullets of some larger diameters so you can get a good fit and bore seal.
Then, there's the fact that there are several nominal calibers which actually have completely different specified bullet diameters. For example, .45 Colt and .45 ACP are not the same diameter, traditionally anyway. Many .45 Colt guns want a 0.454" bullet, or greater. (And if you jump to .45-70s, that's getting up toward 0.459"!) Similar things happen between traditional .44-40 and modern .44 Mag. revolvers.