I noticed that the controls note that mouse button one is primary weapon, mouse button 2 is secondary weapon such as missiles and mouse button 3 is plasma cannon. I have only two buttons on my mouse not counting side buttons. What does mouse button 1, 2, and 3 refer to?

Usually, mouse button 0 refers to left button, 1 is right button and 2 is mouse wheel - yes, you can also click with mouse wheel in case you didn't know.