OSGi allows for having packages split across multiple bundles. This, together with a dropins mechanism, is a true mine field.
So, what's wrong with those split packages? They are split! OSGi, in some magic way, merges them during runtime, but does not see explicit dependency between bundles providing those packages.
The P2 reconciler app, using some Equinox service, refreshes all packages that have dependency changed. So, for example, if you install a bundle providing javax.xml into dropins, you'll have almost all plugins refreshed (depending on the dependency tree).
But, since bundles with split packages are not dependent on each other, you may end up in a not so much theoretical situation, were a bundle with one split package is refreshed, and the other is not. If they do depend on each other (f.e. one has an implementation, the other an interface) you will get a nice ClassCastExceptions or other, similar runtime errors.
Real Eclipse bug can be found in the Eclipse bugzilla.