Raffi orders Rios to stay on La Sirena and check the systems for Borg infiltration. Rios is a Starfleet captain. Raffi is a Commander. Raffi cannot give Rios orders.
Rios' rank is Commander. He is the highest ranking officer on his ship, and therefore has the position of captain of the ship, but his rank is still Commander. Raffi is also a Commander, but her position within Starfleet gives her nominal authority over Rios.
Rios' rank is Commander. He is the highest ranking officer on his ship, and therefore has the position of captain of the ship, but his rank is still Commander. Raffi is also a Commander, but her position within Starfleet gives her nominal authority over Rios.
Ricardo asks the replicator for "four cakes." He is instead given four slices of cake, which is not what he asked for. Also, he never specified what type of cake and is given four different kinds. Replicators require more specific input and are more precise in their output.
In the FBI agent's flashback, one of the Vulcans visiting earth performs a mind meld with him in the 1980s, but mainstream Vulcans would not use mind melds for hundreds of years as depicted on Star Trek: Enterprise (2001). Unless these Vulcans were part of the breakaway sect (rather than the mainstream Vulcan society), this should not have occurred.