You need to provide way more information here.
Plus your test script could never work. is_file(file) is missing a $

The bug is real. I not have cut and paste.

That may be, but then you need to provide something we can go on.

for example:

    strace -o out php -r 'echo is_file("/bin/sh");'

Then in the out file, look for /bin/sh. On my Linux machine I see:

    stat("/bin/sh", {st_mode=S_IFREG|0755, st_size=113112, ...}) = 0
    write(1, "1", 1)                        = 1

The = 0 means the stat succeeded and then PHP writes 1 to the out. If this doesn't work on your system you have a filesystem-related problem of some kind. It is extremely unlikely that this is a PHP bug since all it does is do a stat() syscall under the covers.

the line is identical for you
i have tested
    
    $file = "ephp/out";
    if(is_file($file)){
        include ($file);
    }

not include out

is_file("namefile.php") found
is_file("ephp/out") not works

$file = "ephp/eph_".$comando.".eph";
if(is_file(dirname(__FILE__)."/".$file)){
      require ($file);
} // works

So look at the system calls and figure out why it isn't finding the file.
There is no PHP bug here.