First, and more game impacting:

A Progen with Shield Restore on auto-use, when its shields hit zero, will use it, but it will keep attacking and lose its ‘focus’ (stopping the regen).  If the player clicks it, mid-attack, the ship will stop firing and use it correctly (unless told otherwise).

Second, and super minor:

The tool-tip for adding to the bounty on someone does not update the "next increment" amount when you research the Advent (not sure if the other races have one) ability that increases the bounty per 250cr paid.