I found a similar ticket filed against STASH (https://jira.atlassian.com/browse/STASH-3529) and used it for this one since they did a much better job outlining the problem.

merge commit messages result in duplicate time entries in JIRA when using Smart Commits.
Steps to reproduce:
Create a branch and commit a change with "KEY-123 #time 10m"
Create a pull request for the branch and merge it
The merge commit that Stash creates will contain "KEY-123 #time 10m" again
20 minutes will be logged against issue KEY-123
Expected behaviour:
Only 10 minutes should be logged against KEY-123