If dice have bad enough quality control, they can roll poorly. I've seen d6s that have come with some board games that were definitely not fair dice--not intentionally, of course, just very poor craftsmanship. However, this is always pretty obvious, and I've never seen this problem with the boxes of D6s sold at my local game store. Assuming the dice are evenly weighted, and have square faces that are regular and even corners and so on, there's nothing to worry about. And this WILL be the case (that the dice are fine) absent very poor QC or someone intentionally meddling with them.
For what it's worth, there is probably some amount of deviation from exact randomness with regular dice given how most people roll them and their QC, but it's very small and probably not predictable. The only thing I could think of in a normal set of dice that would cause it to diverge from average rolls would be the fact that the pips on the dice are made by scooping out chunks of the dice. So, the side with six pips might be lighter than the side with 1 pip, for example, throwing off the center of gravity of the dice. Most dice fill in the pips with ink or paint though to counteract this, and I imagine the effect is relatively small.
Usually, I use a set pretty hefty sharp-edged dice with numerals rather than pips, because they are fun to throw and will be weighted evenly. But when playing my Orks, I use a bunch of small, light, non-fun-to-throw pip-dice because I sometimes need to roll 100 attacks at once and don't want to throw my 12 heavy dice 10 times. However, even if they're light and kind of boring to throw, the fact that i'm rolling 100 of them at once makes up for it.