After updating the github branch source plugin and Jenkins, I noticed that suddenly our old PR's without Jenkinsfile's started building.  I looked in the Scan Repository Log and saw it saying:

‘Jenkinsfile’ found

for PR's that didn't have a Jenkinsfile.

Reverting the plugin back to 2.0.4 immediately solved the problem.

Update:

Looks like [this](https://github.com/jenkinsci/github-branch-source-plugin/commit/8272f20a872ce4fbafb6417b00bdd5aea0a43e7b) caused the behavior change.