Merge commit messages usually contain all commit messages from one branch. This includes the exact text from any Smart Commits included in the merge, causing all commands to be executed a second time.

i understand JIRA 7.1 included an improvement where duplicate time entries are ignored, in an attempt to solve the problem of merge commits containing time entries, but the #comment's are still added every time and any status changes (#ready-for-test, ...) are also carried out. The comments are not very critical, worst thing that happens is that it appears someone else adds the same comment I added, a few days after me (when they merge my commits into another branch).

The status changes are dangerous though: if a ticket has since been transitioned to another status which happens to allow transitions back to the Smart Commit's status, the ticket might suddenly be reopened without anyone noticing, and without any indication as to why.

My suggestion: add an option for BitBucket Server to simply ignore merge commits when checking for Smart Commits.