I noticed that when i take the barge from cottonwood to the fort, rex simply vanishes. I cannot enter Caesar's tent since the game thinks hes still following me, but i cant talk to him to get him to stop following me because he vanished into thin air.

Is there a fix for this besides simply not taking rex with you on the barge?

use one of the companion dismissal terminals.
One can be found in the Lucky 38 Casino, by the elevator.
Another can be found on the front of the Gun Runners shack.
Hope this helped.