In some episodes the headphones Phones wears in stingray disappear in the reverse shot then reappears in the front shots.
The use of "Commander" here does not refer to rank but to Commanding Officer which could be any rank that is above the others. Shore's actual rank is not mentioned.
Troy Tempest's rank is Captain, which in naval services is a higher rank than his boss Commander Shore.
The fishing line was used to pull Stingray out of the water is visible in the opening titles.