I know about the cutscene bug that some people have reported and I don't know if this is related or not. This is my first playthrough and I have not met with the exchange yet, and the little bat creature is still talking to me, so I assume I don't have the bug and just need to do more things against the Exchange.

I have fought off the boarders of the Ebon Hawk (the Red somethings?) and went to do other stuff in the Refugee Sector, only to come back and be told I cannot board the Ebon Hawk at this time. Anyone know what gives? Is this a glitch or do I need to go somewhere or do something?

If you got the "invitation" to meet Visqius at the Jek Jekk Tar club, then you need to do that quest. You won't be able to board the Ebon Hawk until you complete that.

 

If you haven't received that invite....Try going back to an earlier game save & trying again.