It just happened for a system update notification. Here is the output (slightly reindented) that shows 2 identical x-canonical-message-actions sections:
$ gdbus call --session --dest com.canonical.indicator.messages --object-path /com/canonical/indicator/messages/phone --method org.gtk.Menus.Start [0,1] ([ (uint32 0, uint32 0, [{'action': <'indicator.messages'>, 'action-namespace': <'indicator'>, 'x-canonical-type': <'com.canonical.indicator.root'>, ':submenu': <(uint32 1, uint32 0)>}]), (1, 0, [{':section': <(uint32 1, uint32 1)>}, {':section': <(uint32 1, uint32 2)>}, {':section': <(uint32 1, uint32 3)>}]), (1, 1, [ {'x-canonical-message-actions': <<@aa{sv} []>>, 'target': <true>, 'x-canonical-time': <int64 1439206717000000>, 'x-canonical-type': <'com.canonical.indicator.messages.messageitem'>, 'x-canonical-app-icon': <('file', <'file:///usr/share/ubuntu/settings/system/system-settings.png'>)>, 'x-canonical-message-id': <'7f97870a-2d8658-2d4da9-2d819f-2d3f503499bc4f'>, 'label': <'Il existe une image du système à jour.'>, 'icon': <('file', <'file:///usr/share/ubuntu/settings/system/icons/settings-system-update.svg'>)>, 'x-canonical-text': <'Appuyez pour ouvrir le gestionnaire de mise à jour du système.'>, 'x-canonical-subtitle': <''>, 'action': <'ubuntu-system-settings.msg.7f97870a-2d8658-2d4da9-2d819f-2d3f503499bc4f'>}, {'x-canonical-message-actions': <<@aa{sv} []>>, 'target': <true>, 'x-canonical-time': <int64 1439206717000000>, 'x-canonical-type': <'com.canonical.indicator.messages.messageitem'>, 'x-canonical-app-icon': <('file', <'file:///usr/share/ubuntu/settings/system/system-settings.png'>)>, 'x-canonical-message-id': <'7f97870a-2d8658-2d4da9-2d819f-2d3f503499bc4f'>, 'label': <'Il existe une image du système à jour.'>, 'icon': <('file', <'file:///usr/share/ubuntu/settings/system/icons/settings-system-update.svg'>)>, 'x-canonical-text': <'Appuyez pour ouvrir le gestionnaire de mise à jour du système.'>, 'x-canonical-subtitle': <''>, 'action': <'ubuntu-system-settings.msg.7f97870a-2d8658-2d4da9-2d819f-2d3f503499bc4f'>} ] ), (1, 3, [{'action': <'remove-all'>, 'label': <'Tout effacer'>, 'x-canonical-type': <'com.canonical.indicator.button'>}]) ],) -- You received this bug notification because you are a member of Ubuntu Touch seeded packages, which is subscribed to indicator-messages in Ubuntu. https://bugs.launchpad.net/bugs/1473029 Title: notification (image update, gmail, calls) displayed twice Status in Canonical System Image: New Status in indicator-messages package in Ubuntu: Confirmed Bug description: current build number: 54 device name: arale channel: ubuntu-touch/rc-proposed/meizu.en last update: 2015-07-09 08:43:49 version version: 54 version ubuntu: 20150708.1 version device: 20150706-a9e00a0 version custom: 20150707-800-5-34 Sometimes notifications are displayed twice in the indicator. It happens randomly with all kind of notifications (image update, gmail, calls) Push client logs shows a single notification. There is nothing specific to reproduce, sometimes it happens, sometimes it doesn't. To manage notifications about this bug go to: https://bugs.launchpad.net/canonical-devices-system-image/+bug/1473029/+subscriptions -- Mailing list: https://launchpad.net/~touch-packages Post to : touch-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~touch-packages More help : https://help.launchpad.net/ListHelp