I have a global ~/.hgignore in addition to an .hgignore in my repo. I set up the global ignore like this: http://choorucode.com/2013/02/02/how-to-have-a-global-hgignore-for-mercurial/

In my global .hgignore I have:

\.rej$

SourceTree listed a .rej file among my repo's "uncommitted changes". I guess it's ignoring my global ~/.hgignore file, and only looking at the project's .hgignore? I was able to work around this bug by adding the same line to my project's .hgignore.