Hmm, as a workaround, perhaps try reloading if a support ship is available. Or you could just skip the mission.
Basically, it teaches you that you have to wait for lockon to shoot, cause it won't hit otherwise unless you're extremely lucky. Also, there is a wait count (3 for Interceptor) before you can fire again. Also, Interceptor is aspect seeking, that is, it tracks towards the point where it and the target would intercept given the target's current speed & heading, vs. chasing the tail, like the MX-50/Rockeye does. In a nutshell. Although, it would be nice to find the problem... wait for Gooby or someone, I guess.