Audio problem: When Newton is telling Stacker what he saw when he drifted with a Kaiju brain, his lips don't match what he's saying in some shots.
Audio problem: When Dr. Newton and Hermann are with the baby Kaiju, Hermann says "Should be three," but his lips aren't moving at all.
Chosen answer: Most likely they only use it when they know they have a guaranteed shot and won't waste it. It can't be reloaded that easily. Like having one bullet to kill a zombie vs a sword so go for the sword save the bullet it's more valuable. That's typical military tactics. Possible firing whatever weapons could cost a ridiculous amount of money just like missiles do. It's not exactly like Yeager weapons were mass produced they are all different. Last reason is reducing extra casualties by making sure they don't miss when they fire or making firing weapons the last resort. And just for the movie's sake it would be boring as crap if they just blew the heads off in seconds.