I daresay it may have been an accidental reference; it's easier than you think to form a reference. For example, if you have package A installed, and you're developing package B, and package B has a page layout that includes a custom link or custom field from package A, then you've automatically formed a reference.
The reference doesn't have to exist in package.xml in order for you to create an extension package. All it takes is any simple configuration anywhere in package B referencing package A and you'll have your reference. Check the list of items in package B, and see if anything there is from package A. It should let you know right on the list.
Your best bet is to uninstall any version of your package where it became an extension (if you've uploaded it/installed it anywhere), and request that salesforce.com roll the package back into a beta on the last version you had where it was not an extension; this should undo the Managed (Extension) status. Short of this, you'll be required to create an entirely new managed package, which will definitely be nothing short of an inconvenience.
Finally, as noted in the comments, you could try uninstalling package A, and see what errors you get. You'll be advised as to which elements caused the dependency.