Probabily this line of the patch notes:
- Fixed Hyperspace Core processing power to normal
Which means, Hyperspace cores were giving 5x processing power like computer cores, but now they don't.
Tested this theory since after my last post I've managed to move my ship away from the upgrade card. Still happens after making sure ship has more than enough Computer Cores to offset the Hyperspace Core balancing.
It seems that the initial ejection of the upgrade in question broke it's state and that then crashes the game as it's sucked back in.