My best guess is that your function does not iterate through the whole matrix, because of the safeguard you worked in order to avoid RunTime Exception:

        if(i !== arr.length-1){
            if(col === row[j+1] || col === arr[i+1][j]){
                counter++;
            }
        }
           else if(col === row[j+1] || col === arr[i][j+1]){
                counter++;
            }   

Probably some values are left out that are found in the last rows of a given matrix.

Demo-code that allows to cycle through the whole matrix without exception:

function solve(matrix) {

    const result = matrix.reduce((acc, currRow, rowIndex) => {
        // return currenCount also possible
        const currentCount = currRow.reduce((acc, currItem, itemIndex) => {
            if (currItem === currRow[itemIndex + 1]) {
                acc += 1;
            }
            // if matrix[rowIndex + 1] is undefined return empty array
            // will throw TypeError if attempting to take element from undefined
            if (currItem === (matrix[rowIndex + 1] || [])[itemIndex]) {
                acc += 1;
            }
            return acc;
        }, 0);
        // console.log(count);
        return acc + currentCount;
    }, 0);

    console.log(result);
}