When using a Freestyle job with a wildcard branch filter, the source of PR's are ignored when multiple branches exist.  So let's say you push changes to branch bugfix/a and then branch bugfix/b both of which were branched from QA.  If you create a PR for bugfix/a, it's bugfix/b that is cloned and compiled and then a second job is queued for bugfix/a.  If the PR is for bugfix/a then it would be expected that it's bugfix/a that is pulled.

Seems to me that the easiest fix would be to populate parameters or env variables with the branch, tag, and Id supplied in the PR payload for dynamic branch filtering.