The problem is that all four buttons are inside the same loop iteration, so $_ is set to the same thing all four times you call it. What you want is something like this (untested):

my @cols = ();
foreach (@files)
{
   $_ =~ s/.*[\/\\](.*)/$1/;
   push(@cols,td(submit(-name => 'file', -value => $_));
   if (@cols == 4)
   {
      print Tr({-alien => 'center'}, @cols);
      @cols=();
   }
}
if (@cols)
{
   while (@cols < 4)
   {
     push(@cols,td('&nbsp;'));
   }
   print Tr({-alien => 'center'}, @cols);
}
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That builds up a row, and prints it when it's finished. For the last row, it creates cells with a single non-breaking space in them, which avoids formatting annoyances in some browsers.