I used to think that was a contradiction. Now I think it's almost inevitable. I wrote more about it elsewhere [1], but the basic deal is that most companies have other priorities than being effective, so the processes that dominate will reflect those priorities.
On average, the first priority of managers and execs is maintaining the power structures that make them a big deal. But true Agile processes are about empowering teams to self-organize around serving users. Ergo, Sturgeon's Law [2] applies here too: 90% of company software process is crap.
I think reason why Scrum in specific won out is that it combined a process framework unthreatening to executives with the multilevel marketing scheme of Scrum certification. Executives got to keep doing what they were doing, the workers got a "didn't stop breathing" certificate, and coaches got paid. Win, win, win!
[1] http://williampietri.com/writing/2011/agiles-second-chasm-an...