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 2.4.8.0.
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?