I have noticed a bug where using certain Klingon ships and activating transwarp either in a system or in sector space causes the ship to instantly transwarp and disappear. Then the animation continues as normal except the ship is then invisible. What is strange is that it does not happen every time. I have no problems with the bird of prey type ships so far, but it usually happens with battle cruisers, specifically the Vor'Cha and Vor'ral type ships. I will have to see if I can capture the bug as a video to better illustrate what is happening.
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To my knowledge whether it happens or not depends on the destination, not the ship. Qo'nos for example, always does it for me.