git commits duplication while rebasing

checkout.txt

anddam@bibook /opt/macports/ports-git d049d33 [1]$ git checkout master
error: Your local changes to the following files would be overwritten by checkout:
        lang/ghc/Portfile
Please commit your changes or stash them before you switch branches.
error: The following untracked working tree files would be overwritten by checkout:
        aqua/MacBiff/files/project.pbxproj.patch
        aqua/doxygen-launcher/Portfile
        aqua/gimp2-launcher/Portfile
        aqua/gimp2-launcher/files/patch-Info.plist.diff
        aqua/nomacs/files/patch-Info.plist.in.diff
        aqua/nomacs/files/patch-crash_on_exit.diff
        aqua/nomacs/files/patch-name.diff
        aqua/qt5/files/patch-firstObject.diff
        archivers/innoextract/Portfile
        archivers/xar/files/patch-configure.diff
        databases/mycli/files/newer_sqlparse.patch
        databases/mysql57/files/patch-lockpool.diff
        databases/pgcli/Portfile
        devel/appstream-glib/files/patch-libappstream-glib-as-store.c.diff
        devel/kchmviewer/Portfile
        devel/kchmviewer/files/patch-avoid-private-member.diff
        devel/kchmviewer/files/patch-encoding-no-abort.diff
        devel/kchmviewer/files/patch-libzip-incpath.diff
        devel/kchmviewer/files/patch-main-mac.diff
        devel/kchmviewer/files/patch-release-build.diff
        devel/kchmviewer/files/patch-use-webkit-and-dbus.diff
        devel/ocaml-menhir/files/patch-Makefile.diff
        devel/shared-mime-info/files/postinstall
        fuse/archivemount/Portfile
        fuse/archivemount/files/patch-archivemount.diff
        games/crafty/files/patch-chess.h.diff
        games/crafty/files/patch-option.c.diff
        gis/grass7/files/patch-libraster_gdal_c.diff
Please move or remove them before you switch branches.
Aborting

log.txt

anddam@bibook /opt/macports/ports-git (null) $ git log -n 20 --all --graph --format="%h %p %d"
* "648c5da 93c7f3e  (upstream/master, upstream/HEAD)"
* "93c7f3e 3c0030d "
* "3c0030d 3ad6584 "
* "3ad6584 1aa3fd5 "
* "1aa3fd5 8fedaa5 "
* "8fedaa5 2e6f4f5b "
* "2e6f4f5b 925275f "
* "925275f 055f8ee "
* "055f8ee 2880805 "
* "2880805 e7e10c2 "
* "e7e10c2 9a52023 "
* "9a52023 176533b "
* "176533b 4f09baf "
* "4f09baf 82a1565 "
* "82a1565 c6433d2 "
* "c6433d2 030b984 "
* "030b984 178e220 "
* "178e220 0ee4ad9 "
* "0ee4ad9 9c46fa6 "
* "9c46fa6 9c3da68 "

reflog.txt

0524116 HEAD@{743}: pull --rebase --autostash mine master: py-sqlparse: add python 3.6 support.
0b70851 HEAD@{744}: pull --rebase --autostash mine master: py-pygments: add python 3.6 support.
3dada8a HEAD@{745}: pull --rebase --autostash mine master: py-crypto: add python 3.6 support.
e094ebc HEAD@{746}: pull --rebase --autostash mine master: py-click: add python 3.6 support.
4114066 HEAD@{747}: pull --rebase --autostash mine master: checkout 41140663733789d27e5be3315859348be4106ef8
fedca06 HEAD@{748}: rebase finished: returning to refs/heads/master
fedca06 HEAD@{749}: pull --rebase --autostash upstream master: checkout fedca06df7b05962ee26de42819546476219b9e3
4114066 HEAD@{750}: checkout: moving from master to master
4114066 HEAD@{751}: branch: Reset to mine/master
fedca06 HEAD@{752}: checkout: moving from master to master
fedca06 HEAD@{753}: branch: Reset to origin/master
06b8497 HEAD@{754}: checkout: moving from fedca06df7b05962ee26de42819546476219b9e3 to master
fedca06 HEAD@{755}: pull --rebase --autostash: checkout fedca06df7b05962ee26de42819546476219b9e3
06b8497 HEAD@{756}: checkout: moving from master to master
06b8497 HEAD@{757}: checkout: moving from fedca06df7b05962ee26de42819546476219b9e3 to master
fedca06 HEAD@{758}: checkout: moving from 1ddaf8fc0f82ed332d4eafb103b01d79726c9710 to origin/master
1ddaf8f HEAD@{759}: pull --rebase --autostash upstream master: checkout 1ddaf8fc0f82ed332d4eafb103b01d79726c9710
4114066 HEAD@{760}: checkout: moving from d049d330b1ec17ca95cf6903509e76489c72e0f1 to origin/master
d049d33 HEAD@{761}: checkout: moving from master to upstream/master
06b8497 HEAD@{762}: rebase finished: returning to refs/heads/master
06b8497 HEAD@{763}: pull --rebase --autostash: ruby-build: upgrade to 20161225
226aab0 HEAD@{764}: pull --rebase --autostash: py-pip: add python 3.6 support.
5201336 HEAD@{765}: pull --rebase --autostash: mycli: add python 3.6 support.
7624453 HEAD@{766}: pull --rebase --autostash: py-six: add python 3.6 support. Use pypi livecheck.
8fd4920 HEAD@{767}: pull --rebase --autostash: py-configobj: add python 3.6 support. Use pypi livecheck.