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Storing a St.Label instance should bump its reference counter. In the offending line, it tries to read "clutter-text" property and call set_text() - I assume segfault happens because St.Label holds a broken reference in the property.
This line (very likely) https://github.com/codito/gnome-pomodoro/blob/75e2f7acb52e26a5abfc8a0a3305dc3c03c7cf54/plugins/gnome/extension/dialogs.js#L647
Causes gnome-shell to crash, you should connect on actor destroy signal and nullify the pointer or just stop the timer.
This is bug has been reported in ubuntu: https://bugs.launchpad.net/ubuntu/+source/gnome-shell/+bug/1714989
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