The reality is that a contributor license agreement is of near-zero help to an open-source project; it's only present here because Nike's lawyers required it. But the surface area of 'contributions that infringe on patents held by the contributor' is infinitesimally smaller than 'contributions that infringe on any patent held by anyone else'.

Non-trivial, inclusion-worthy patches don't just fall from the sky; certainly, if it ever were to happen, you can be sure that other developers will be doing a search for patents issued to that author. If anything were found, the patch author would be advised that the contribution could not be accepted, due to the patent.

If and when a project's developers become aware that a technique used is patented, or even just potentially infringing pending some legal outcome, whatever would have to be ripped out is ripped out. But the patent, and the potential infringement, will not be discussed publicly. Open-source projects can't work any other way - the liability is on the users, not the developers, and it's not in their interest to expose their uses to "willful infringement" liability. Even public discussion of actual or potential infringement in is toxic - you would be asked to stop (privately).

It is what it is. It's also not too problematic, in my limited experience. But that may well simply be because nobody tries to find infringement, for obvious reasons.