One of my towns revolted, as a result the client ruler was kicked out. So it retreated to my fleet nearby. Now my fleet won't move and the client ruler wont get out. This is really bad timing because I have a depleted army with my faction leader who is surrounded and badly out numbered by enemy forces and need to escape quickly. I mean shouldn't the client ruler die if the settlement is lost?

This is really really annoying.
try if this helps:

1) select the fleet
2) select the ships inidvidually in the fleet tab

if you select the ships in the tab, the movement points of the people inside the ship are afaik not counted. You wont be able to remove the client ruler from the ship, but at least you should be able to move the ships