Make a new branch from the master you are merging into. Cherry pick the commit you want to merge into that branch. Then open a pull request for that branch.
Alternately, rather than a full-blown pull request, you could just cherry-pick the commit from one into the other.
Start here, where M1 is the branch you want to merge into, and e
is the commit with the fix you want in both branches:
-M1
-M2-a-b-c-d-e
Simplest is just to cherry-pick the fix:
$ git checkout M1
$ git cherry-pick e
That gets you this:
-M1-e'
-M2-a-b-c-d-e
If you must do a pull request, try this:
$ git checkout M1
$ git checkout -b M3
$ git cherry-pick e
That will get you this:
-M1
\
M3-e'
-M2-a-b-c-d-e
...and once you issue the pull request and it gets merged - most likely a fast-forward merge - you'll be back here:
-M1-e''
-M2-a-b-c-d-e