Right. Think of a new version of some software that drops support for a deprecated part of an API in a minor release. I did get screwed by that happening with a Latex package, xy-pic, some years back.
Yeah. Painful. Thats the kind of thing semantic versioning aims to solve: within a major release, all minor and patch releases must maintain backwards compatibility. Patch releases may not change the API at all; minor releases may add to it but not remove things[1]. Major releases may drop backwards compatibility by removing or modifying API items. Seems like a reasonable system to me and would avoid the problem you mentioned.
[1] I guess it can deprecate things, as long as they are still available for use.
