Navigate to your installation folder:
modules/UpgradeWizard/systemCheck.php
Find the line in the file that initializes the $skipDirs array and add the two folders it mentions in the comment ‘cache’, and ‘upload’, to the array initialization.
// add directories here that should be skipped when doing file permissions checks (cache/upload is the nasty one)
$skipDirs = array(
$sugar_config ['upload_dir'],
'.well-known',
'.svn',
'.git',
'cache',
'upload',
);