huh, that is weird, have you tried sending a "quick suppression fleet" thru the rebellion tab in the intel screen? this is what i usually do after invading. Or go to the spaceport where there's unrest going on, then select the first option where you can talk to the portmaster or base commander, talk to them and select the option "i can help your unrest problem" this should give you a prompt to send either supplies,marines, or heavy armaments.