I think there are 3 big factors at play:
1) Laziness vs. Complexity = Complexity Wins. People screw up all the time setting up software, and unfortunately tracking codes don't throw big red error messages! No CEL here.... Everyone's guilty of this at one point or another. Unless you have a very small site, there's probably multiple templates, Ajax or Flash content becomes a black hole, broken links, non-canonical urls, etc. etc. these can all skew things. It is hard work to really keep an up-to-date, complete accounting of everything on your site(s).
Corey (first poster above) is right - you gotta have a few methods going on together to audit and keep things reasonably close, but while, yeah, you need to do server stats - his example shows why you also need to do JS stats. It's great to know you're about to have 30k+ pages show up on google (woohoo!!!) but if your boss thinks you just got 30K eyeballs, well, that's bad news for you next week.
2) Terminology , or "lies, damn lies, and statistics". I still run into clients who are counting hits and not pageviews, not counting unique visitors, etc.
The thing is, even those stats are pretty meaningless unless you look at the whole funnel. For instance, I like to show my SEM clients how I do searches.
I enter a queries, right click to open into tabs on 5-10-15 results, whether organic or PPC, and only then start looking at results. I'm my own worst nightmare (but Google loves me!) - all those sites are going to see me hitting in and then spending a minute, 2 minutes, 15 minutes, who knows how long, on the homepage... half the time I'll find what I'm looking for half way through the stack and close out the rest of the tabs.
Honestly, for me that's become a HUGE bad habit. I'll have upwards of 70 tabs open sometimes. I'm a bad example, but that sort of behavior and other things like it has to be skewing #s.
3) Incentives - This, I think is the biggie. Anyone who gets analytics and tracking, and is pushing it, selling it, or buying it has a vested interest, and it's easy to fall into the trap of reading what you want to read. This may or may not cross over to unethical behavior, but it is difficult for people to stay unbiased when there is big money on the line.
I think the whole clickfraud issue got a bit overblown from this very aspect - even these 3rd parties have a vested interest in finding fraud, whether it's real or not. If they don't find any, how are they going to justify continuing operations?
Unfortunately I don't see a really good way around this without major client-side tracking (read as: horrible invasions of privacy) getting a firm foothold. If someone could develop a truly privacy-protecting, double-blind tracking plugin for firefox/IE, etc and license the info on particular sites to trusted stakeholders, then that'd be fantastic... but I don't see that anywhere in the pipeline.
Personally, and in my business, I think the best answer for the near term is regular open communication between client and vendor. We 're pushing hard on paid SEM for dealers, and we're running into a lot of misinformation, bad websites, and bad internal tracking.
From our POV, the only statistic that matters in the end is the bottom line, and we feel we just need to go beyond what might normally be expected to make sure that this traffic is turning into leads for sales staff, and at the end of the day, that staff knows which leads we provided, and that we want to help them as much as possible. I know that sounds sickeningly warm and fuzzy, but it's really just watching out for ourselves. Yeah, someday we might screw up and our numbers will be wrong, or a competitor could come in strong and try to make us look bad, but no matter what happens with that, it's tough to argue with regular visits, checkups and phonecalls.