Since 2.7 added a new feature to upgrade the plugin right through the Plugins page in Dashboard, it's indeed a convenient function. However, I came across a problem with this new funtinon today.
I use Backlinks.com,a link-selling site to earn the fee of my sharing hosting. It offers a plugin named backlinks to active the ad links area in the blog. Today when I opened the Plugins page I found there is upgrade available for this plugin. So I used the auto upgrading function and then "crack!", it turns out that the new backlinks plugin is not the one I sells links with.
I have to admit that it's my fault that I didn't see through the version details before upgrade. And it's a lesson to else people. I wander if there should be some mechanism to make sure the plugin is Unique? Maybe wordpress could setup a site to generate unique ids for the plugin writers.