Zilla Jr was losing alot of blood, he knew he had to return to the bottom of the ocean to recover, but he decided to just continue following Amblygon. After all, he would heal from his wounds on the way, and when he heals from his wound he will be stronger than before. Godzilla knew what he had to do, he had to start following Zilla Jr, despite Zilla Jr being a strong kaiju more than capable of fighting, he isnt as experienced as Godzilla in combat, he cant estimate another kaiju's capabilities like Godzilla. Godzilla had to start following Zilla Jr, but he had to take care of Aurora [Zilla Jrs mate] in the mean time. Once she was healthy he could start following Zilla Jr.
Amblygon had underestimated Zilla Jr too. He knew he had approached too eagerly and fought too confidently. He needed to continue moving away from Zilla Jr and as fast as possible without any rests