The history pane displays a revision number next to each commit that touched a file. These revisions are numbered starting from 1, based on the commits we receive from git. However, we set a limit of 1000 commits when making the request, so if we hit this limit these numbers don't line up with the actual number of changes to the file. For example, see https://cs.chromium.org/chromium/src/DEPS.
This can be confusing, because you'd expect the revision labelled "1" to be the first commit touching a file. The nature of git means that we can't easily tell how many commits we're missing, but it would be nice to display something at the bottom of the history pane to indicate that there are earlier commits not being displayed.