I was in the process of performing a Micro Warp Jump when the ship mutinied. This kept the skill target selection up, however I was unable to select a target. After crushing the mutiny I reselected the Micro Warp Jump skill and performed it, after doing so I ended up with the ship model and marker separated as seen here. Haven't seen it happen since.
0_1544370749787_BattlefleetGothic2-Win64-Shipping_2018-12-08_18-45-17.jpg