I'm not actually sure if this is a bug in SourceTree or in Bitbucket, but since it's both Atlassian I trust this ticket will find its right place.

When I right-click a feature/... branch in SourceTree, then click 'Create Pull Request...', check the values in the dialog and click 'Create Pull Request On Web', Bitbucket opens in my browser with this error message: "Commit 'feature%2Fmy-branch-name' does not exist in repository 'MyRepo'" (with the correct branch name and repository name, but with the '/' replaced by '%2F').

The url SourceTree seems to have used to get there is this: https://bitbucket.example.com/projects/mr/repos/myrepo/pull-requests?create&sourceBranch=feature%252Fmy-branch-name

Note the '%252F' in that url, seems like a case of double url encoding in SourceTree where only single url decoding is applied by Bitbucket. If I change the url to https://bitbucket.example.com/projects/mr/repos/myrepo/pull-requests?create&sourceBranch=feature%2Fmy-branch-name the feature works correctly.