Edited because the question does not appear to carry the date asked.
This has been reported by several of our developers over the last couple of years and it happened to me. I'm using Sourcetree 18.104.22.168.
This morning in response to a pull request on a branch I did not have local, I checked it out from origin and tried to test the changes. After a few minutes of troubleshooting an error I discovered I had four commits to pull, three of then dated 6 Apr (today).
Could Sourcetree be tracking commits on branches you've never checked out?
What other reason would checking out from Origin not include all commits?
Git will checkout the branch from its local copy of the repository, if it has a copy. So if you did a fetch before the 6th April your local copy will have been aware of the branch, when you checked out you got the version pre-6th April and then Sourcetree indicated there were new commits post 6th April
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