At least for Mercurial-based repos, if revision B depends on A, modifying B and running "arc diff" will put the changes from A into the revision for B. While this can be easily worked around by specifying the base commit, it would be preferable if arcanist/phabricator determined the base commit for B by default.
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I believe the behavior as described is (currently) expected with Mercurial. To update revision B without A's changes you must specify the commit from A to B, otherwise it will default to the range from master to B which will include A's changes.