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Generally it happens because the e-book process is still not fully integrated into major publishing systems.
In most big publishers, e-books are either created from the original (computer-set) text, or scanned and OCR'd after the print run. But in either case, the digital text must be checked and proofed, just as the press material was proofed... and in most cases, it is not. Publishers are still putting more effort into proofing printed material than digital material, and in many cases, doing no digital proofing at all.
Most of them probably see the step as unimportant, since they see so little inherent value in e-books (or cannot yet figure out their profit from them) that they assume them to be little more than a loss-leader, and therefore choose to spend as little money and attention as possible on them.
When digital material is better-integrated into the publishers' standard procedures, we should expect better proofing of all material, on a par with printed material. For a lot of publishers, this will likely not happen until e-book business models are better-established, and they can begin to work out reasonable budgets and cost-effectiveness for their production needs.
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