I showed this ticket to the team and one of the guys commented this:

Leandro Loos @alexei.znamensky: from what I saw, when we configure a job that finally succeeds, it comments on all the tickets for which a job was configured and failed
Leandro Loos and once it posts the message on those ticket it "clears" it's pending list to post and starts all over
it's the pattern I noticed

I have not run that test yet, but it might be a pointer to the problem.

As a matter of fact, the job 1806 message went to 4 tickets: one that appears to be the right one, and then other three had no messages whatsoever, but the job runs used in them had all failed.

This sounds like the same issue we are facing (using Jenkins version 1.598 and JIRA plugin version 1.38).

What I've noticed is that the incorrect updates have only the first line of comment, e.g.
"SUCCESS: Integrated in DEV-16-2 #455"
whereas a legitimate update will include the full changeset description on subsequent lines.

In my view this issue should have a higher Priority than Minor/Trivial as users are being misled into believing that changes have been included in builds when they have not been.

Hi alexeiz,

Just curious, what version of Jenkins and JIRA plugin are you seeing this issue in please?

As I said, I'm seeing the issue with JIRA plugin version 1.38 and I wonder if it is resolved in a later version.

Thank you for your update, alexeiz.

We are seeing two different formats to the message. A valid message has multiple lines including the JIRA reference, commit comments and changeset details. Incorrect (misleading) messages contain a single line “SUCCESS: Integrated in PROJECT #BuildNum”.
The following image shows a good followed by a bad message as seen on a single JIRA ticket:

We are using Jenkins version 1.598, JIRA Version v6.3.15 and JIRA plugin version 1.38.

Can someone please confirm whether this is a known issue?

Is this possible that there were concurrent builds running on the same jenkins slave when this happened?

Thank you for your response, Radek.
That is possible, yes, as we do tend to have a number of builds running concurrently on the same slave.
I have tried to investigate some recent examples but I'm struggling to find a pattern.
I can only add that the issue is still happening. The "wrong entries" tend to follow some days after a valid entry in an earlier build of the same job. By this I mean we may have a valid (full) comment stating "Integrated in QA-17-1 #22" followed some days later by an invalid (abbreviated) comment "Integrated in QA-17-1 #23" (and some days after this a further an invalid comment "Integrated in QA-17-1 #28"). QA-17-1 builds are run once per day.

Interesting, so this might some other issue too, did you try with the latest version?

A month ago we upgraded to Jenkins 1.651.3 although we are still using JIRA plugin version 1.38. I acknowledge that I should consider updating to a newer version of the plugin.

In the meantime I should update an earlier response I posted – we do NOT use concurrent builds. Apologies for the misinformation. Also, apologies for the delayed response - I don't get the time I need to focus on this issue.

Still thinking about it... could this be anyhow related to JENKINS-32884?

Just to say that we're now on Jenkins 1.651.3 with Jira plugin v 2.3.1 and JIRA v7.2.7 and we still face this issue. We upgraded the Jira plugin a couple of weeks ago and initially I thought that the problem was resolved. However, there is a specific Jenkins job/project which has been hit three times in the past six builds. These builds have erroneously flagged some 1200+ JIRA tickets as having been included in the build and this has added around 80 minutes to the build time.

I think I'm going to switch the option off for this specific job as people have reported being flooded with JIRA e-mail notifications.

I've been looking into this further and trying to work out why some builds have posted comments to cases which are not in the build manifest. I noticed that for the affected builds they each have "Changes in dependency" showing under the Changes. I now see the help text "Selects all issues found in change lists or parameters of current build or in any of changed dependencies." for the Issue selector parameter of the "Update relevant issues" build step and I'm wondering if this is the source of my problem.
 
Can anyone point me to any documentation for this parameter, please? I wonder if it is the "changed dependencies" that is throwing out all the unwanted JIRA comments and whether I could use an "Explicit selector" instead.
 
Any help would be gratefully received.