At most of them it just meant that HR ended up wasting time dealing with crappy tools, which is no big loss, since HR is a usually a waste of oxygen anyway. At Disney and Amazon, it meant that the people producing consumer-facing content wasted a lot of time fighting the tools that were supposed to enable their jobs, and a lot of developers had to waste a lot of time supporting the tools that weren't doing their job.
For example, just two and a half years ago, one of the buyers at Amazon showed me how she set up the relationships so that when you look at an iPod, you get a collection of compatible accessories. She had to create relationships for EVERY permutation between each accessory and for each accessory to the iPod. By hand. In a spreadsheet (Excel, I think.) Then she uploaded it to the site, and every once in a while a relationship would mysteriously fail, because of another relationship managed in another tool that she had no access to conflicted with it.