Ships are getting stuck in alt-mode during and after combat when using the Transformation mechanics, and ALL Seperation Console Pets do not return when recalled during combat and after being disabled making those consoles and mechanics pointless and fatally broken!!
"You don't want to patrol!? You don't want to escort!? You don't want to defend the Federation's Starbases!? Then why are you flying my Starships!? If you were a Klingon you'd be killed on the spot, but lucky for you.....you WERE in Starfleet. Let's see how New Zealand Penal Colony suits you." Adm A. Necheyev.
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Dev's don't respond to tickets, and this is on purpose.
But yes, this issue is long standing on any ship that uses Transformation as well as Sep. Pets.