This causes two issues. It is incompatible with the new JIRA 6.2 increased git integration, and causes problems with rebasing
In JIRA 6.2 issues will now sure the number of commits against each issue. When using Bitbucket's branch functionality, the empty branch commit is counted as a commit by JIRA. Therefore, it appears that there was code committed against an issue, when actually only a branch was created.
When rebasing the branch, the rebase will fail unless the branch commit is marked as skip.