For github to auto-resolve an issue on a PR merge it needs text similar to "fixes #XX" in a commit or the PR title.
For waffle.io to associate a PR to an issue it needs the issue(s) in the TITLE of the PR as "#XX".
Because of this I recommend in the title of PR's we try to put "Fixes #XX..." somewhere. You can edit PR titles after they're created. This makes the "pending pr merge" column in waffle go away and manages linking issues to PR's for both waffle and github.