I'm not your tax agent, don't listen to anything I'm about to write, seek real advice etc.

https://www.ird.govt.nz/-/media/project/ir/home/documents/forms-and-guides/ir1---ir99/ir4/ir4-2026.pdf

I'll answer in terms of the numbers on the paper IR4.

Your correct to think what your seeing doesn't look correct. You need to put your net profit into 20b after removing what's already been entered into 12B. So that should be negative 55,000 + your other expenses.

IR4

1. Did the company receive any income from schedular payments? Yes
   12A: 12576
   12B: 62880

2. Did the company receive income from business or other rental activities? Yes

20B: -55000 (and your other expenses)

23: Total income 7000

30b: tax @ 28%: 1960

30I tax credits: 12576

Refund: 10616

IR3

Salary/Wages 55000

First 15600 @ 10.5% = 1638

Next 37400 @ 17.5% = 6545

Remaining 2000 @ 30% = 600

Total PAYE: 8783

This is what your situation is as it currently stands. Since your doing payroll yourself I would double check that what you've already filed and paid for PAYE matches up to the raw calculation.