Other mistake: In the scene from Mako's memory, the terrified little girl stops crying and smiles when Pentecost emerges from the Jaeger's head/cockpit. But if the Jaegers are 250 feet tall, how could she possibly have seen him? It's not kneeling when she looks up at him.
Other mistake: Near the end of the movie, Mako swims to the unconscious Raleigh's survival, blows the top shield of his survival pod, removes his helmet and checks for a carotid pulse...while wearing gloves. No wonder she thought he was dead.
Other mistake: Right after Otachi sprays acid, Gipsy reaches in its mouth to pull its tongue out, but doesn't get affected by any.
Other mistake: During the triple event, different war clocks times are different. One that is stopped and the one that wasn't reset.
Other mistake: When Crimson Typhoon's head is pulled off, their location should not be visible on the radar behind Stacker.
Other mistake: The war clock during the triple event does not reset as it should when a Kaiju breaches.
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.