Our workflow is generally:
# Differential is submitted.
# Differential is accepted.
# Someone with access to the master branch merges the branch specified in the differential and pushes to the remote.
It seems that after upgrading Phabricator last week, differentials are no longer being autoclosed. A general description of what is happening is as follows:
# Branch `X` consists of two commits (`A` and `B`).
# Branch `X` was submitted to Phabricator as a differential (lets say D123).
# The differential was accepted.
# Branch `X` was merged and pushed. Let's say that commit `C` is the merge commit ("Merge branch X into master").
The differential has been updated with links to the two commits (`A` and `B`) on the master branch, but the differential has not been closed.