That isn't an issue with DNN but with Windows. Did you upgrade on Windows 8 or Windows 2012? Newer versions of Windows is known to have issues extracting the files due to security. Before you extract the install you need to make sure the zip is unlocked.
Another cause for that is if the install ran into a problem or if you didn't follow the correct upgrade path. For example, you can't upgrade from DNN 4.9.5 to 7.2.2 directly. It should be that simple, but it isn't. DNN Corp. may want to have some validation in the install that verifies the current version and what they are upgrading to to prevent those confusions. For now, you need to follow a specific upgrade path. Ex: 5.6.8 to 6.0 to 6.2 to 6.2.8 to 7.2.2. That seems to work the best for me.
There are other situations that may cause problems. If you have a user base with 200,000+ users you will need to disable the auto assignment before you upgrade. I think the issue is in 6.1.0 where it changes the description of the Subscriber and Registered User Roles, that triggers ASP.Net Membership to update all of your users and if you have a lot of users then it's very possible that your install could time-out and won't complete....causing a lot of issues.
If your portals have a lot of files in the root directories then you'll also run into problems during 7.1.0 when the Content Manager attempts to index the files. However, that is a much bigger problem, if you manage to get past the install you will have serious performance problems on specific pages of your site that could crash the entire system. In this case, you will need to either modify the core to limit the index to 200 files or move the files to a SANS or a cloud provider.
The issues I run into are not the norm and only a problem for enterprise level companies with massive amounts of data and content. In your case, I bet the zip file just wasn't extracted correctly due to Windows security. Or... you didn't follow the upgrade path.