This script shows that we need to add round() before applying floor() in the Slippy Map Tiles' lat2tile() function. We also need to add (int) to avoid '-0' values. The bug is because PHP uses double-precision floating point numbers (https://stackoverflow.com/a/1863740/1094271)

tileConversionBug.php

<?php
/**
 * This script shows that we need to add round() before applying floor() in the lat2tile() function. We also need to add (int) to avoid '-0' values.
 * The bug is because PHP uses double-precision floating point numbers (https://stackoverflow.com/a/1863740/1094271)
 */

 $tiles = [];
 //Demonstrating only till z3, you can increase if you like
for ($zoomLevel = 0; $zoomLevel <= 3; $zoomLevel++) {
    $tiles[$zoomLevel] = getTilesCount($zoomLevel);
}

print_r($tiles);

function lon2tile($lon, $zoom) {
    return (floor(($lon + 180) / 360 * pow(2, $zoom)));
}

//Function originally from https://wiki.openstreetmap.org/wiki/Slippy_map_tilenames#Lon..2Flat._to_tile_numbers_5
function lat2tileOriginal($lat, $zoom) {
    return (floor((1 - log(tan($lat * M_PI / 180) + 1 / cos($lat * M_PI / 180)) / M_PI) / 2 * pow(2, $zoom)));
}

//Fixing this by rounding before floor, and casting as (int)
function lat2tileFixed($lat, $zoom) {
    return (int)(floor(round((1 - log(tan($lat * M_PI / 180) + 1 / cos($lat * M_PI / 180)) / M_PI) / 2 * pow(2, $zoom),1)));
}

/**
 * Get number of tiles for whole map
 * @param int $zoom
 * @return int number of tiles
 */
function numTiles($zoom)
{
    return pow(2, $zoom);
}
/**
 * Get longitude from tile x value
 * 
 * @param int $x
 * @param int $zoom
 * @return float longitude
 */
function tileToLon($x, $zoom)
{
    return $x / numTiles($zoom) * 360.0 - 180.0;
}

/**
 * Get latitude from tile x value
 * 
 * @param int $y
 * @param int $zoom
 * @return float latitude
 */
function tileToLat($y, $zoom)
{
    $n = pi() * (1 - 2 * $y / numTiles($zoom));
    return rad2deg(atan(sinh($n)));
}

function getTilesCount($zoom) {
    global $landOnlyKV;
    $top_tile = 0;
    $left_tile = 0;
    $bottom_tile =  numTiles($zoom)-1;
    $right_tile =  numTiles($zoom);
    
    //tile count by z level
    $tilesCount = 0;

    for ($x = $left_tile; $x < $right_tile; $x++) {
        for ($y = $top_tile; $y <= $bottom_tile; $y++){
            $tilesCount++;
            //original Tile ID
            $v1 = "$zoom/$x/$y";
            
            //buggy conversion
            //convert to lat/lon
            $lon = tileToLon($x, $zoom);
            $lat = tileToLat($y, $zoom);
            //convert back to tile at z7
            $newX = lon2tile($lon, $zoom);
            $newY = lat2tileOriginal($lat, $zoom);
            $v2 = "$zoom/$newX/$newY";

            //patched conversion
            $lon = tileToLon($x, $zoom);
            $lat = tileToLat($y, $zoom);
            //convert back to tile at z7
            $newX = lon2tile($lon, $zoom);
            $newY = lat2tileFixed($lat, $zoom);
            $v3 = "$zoom/$newX/$newY";

            if($v1 != $v2 || $v1 != $v3) {
                echo "{$v1},{$v2},{$v3}\n";
            }
        } 
    }
    
    return $tilesCount;
}