Eagles six, nine, and ten are sent out to intercept the Voyager. Later, when the alien ships are approaching, they're announced as Eagles four, six, and ten.
Close-up shots of the Voyager's rear rockets shooting out Freon reveal droplets dripping out of the model. Re-positioning of the camera would've hidden it behind the spray.
On the Main Mission viewer, Voyager is represented by an indistinct green dot moving across the upper right corner of the screen. This image is continually recycled despite that it is getting closer to the base.
At about 22:10, after Dr. Linden is knocked unconscious by his assistant, Jim Haines, you can see a propmaster's hand manipulating a smoke maker at the bottom left corner of the screen.