print_matrix.py

from io import TextIOWrapper
from sys import stdout
from typing import List


def print_matrix(matrix: List[List[int]], file: TextIOWrapper = stdout) -> None:
    width, height = len(matrix), len(matrix[0])
    # max length for beautify
    l: int = len(str(1 + max(
        width,
        height,
        max(map(max, matrix))
    )))
    h = len(str(height))
    # print column index

    file.write(
        " " * (h + 1) + " ".join(str(i).rjust(l) for i in range(width)) + "\n" +
        "\n".join(
            str(y).ljust(h) + ":[" +
            " ".join(str(x).rjust(l) for x in matrix[y]) + "]"
            for y in range(height)
        ) + "\n"
    )

строку
h = len(str(height)) - 1
нужно заменить на
h = len(str(height+1)) - 1