On Chrome OS 59.0.3057.0 ToT build @ #460775
(1) Install a V1 app, like Secure Shell:
    https://chrome.google.com/webstore/detail/secure-shell/pnhechapfaindjhompbnflcldabbghjo?hl=en
(2) Pin the app to the shelf from the app list
(3) Run the app (in a tab)
(4) Unpin the app from the shelf while the app tab is still open
(5) Close the app tab
Expected: The shelf item is removed (it has been unpinned and is no longer running).
Actual: The shelf item remains on the shelf.

This defect has probably been around for a while, but bisect might help.
This came up while drafting https://codereview.chromium.org/2790803002
 

V1 app shelf items are not removed if unpinned then closed while running in tab

On Chrome OS 59.0.3057.0 ToT build @ #460775
(1) Install a V1 app, like Secure Shell:
    https://chrome.google.com/webstore/detail/secure-shell/pnhechapfaindjhompbnflcldabbghjo?hl=en
(2) Pin the app to the shelf from the app list
(3) Run the app (in a tab)
(4) Unpin the app from the shelf while the app tab is still open
(5) Close the app tab
Expected: The shelf item is removed (it has been unpinned and is no longer running).
Actual: The shelf item remains on the shelf.

This defect has probably been around for a while, but bisect might help.
This came up while drafting https://codereview.chromium.org/2790803002