In the flashback, the gophers not only fought against Wynyard and his commanding officer, Jim, but they also captured, tortured, and even tried to re-educate them. They also killed two of their friends; Eight-Ball (by impaling his head on a stick) and Chuck (by cutting off his legs and eating them for dinner).
The gophers' final torture for the two frogs involved taking a gun to their heads, and pulling the trigger, so that they could kill themselves. After they refilled the guns, Wynyard pulled the trigger, but missed; causing the bullet to bounce off all of the pots and pans that were in the same room, killing the gophers that were torturing them.
Wynyard and Jim escaped, but they soon found out that another group of gophers were following them. To make things worse, Jim fell down a pit, and Wynyard ran off in fear, leaving him to be killed by the gophers. This put Wynyard in a great stage of guilt, and, while he spent 6 months in a Saigon hospital, became hooked on every barbiturate known to man.
Even though most of the gophers appeared in the flashback, one of them appeared as an illusion when Wynyard (who was high on the drugs he bought from Trevor) was performing his knife-throwing act with Robert (who he mistook the illusion for).