What version are you running?
2.0.20.
What's the URL of the page containing the problem?
https://reviewboard.mozilla.org/r/18627/diff/3-5#5
What steps will reproduce the problem?
Not entirely clear, but something like

1. Upload patch.

2. Rebase commit on top of some committed changes.

3. Update commit with changes around those added in the rebase.

4. Upload patch again.
What is the expected output? What do you see instead?
The interdiff and diffs should ignore the rebase changes.  Instead, while the diffs correctly suppress the rebased changes, the interdiffs sometimes show them.
What operating system are you using? What browser?
OS X 10.11, Firefox 41.0.1.
Please provide any additional information below.
See also https://bugzilla.mozilla.org/show_bug.cgi?id=1212106. smacleod tells me that this may be the interdiff algorithm failing.  Whatever is happening, it's rather unexpected and confusing.