When a ship with a toggled ability is captured, that ability is locked in whatever state it was in at the time of capture.

Specific example: I was playing as the advent loyalists and having a jolly good time of capturing enemy fleets with the titans subjugation ability. I noticed some Vasari Sentinels that I had captured were stuck in their discharge phase missile mode, rendering these ships permanently immobile. I'm not sure if this issue exists with other methods of capture, but my guess would be yes.

Possible solutions:

1) Ensure all abilities are deactivated during the capture process.

2) Captured units retain their abilities.