Here is a small, complete program which demonstrates the problem:

use strict;
use warnings;
# Some file is created by a different process
my $file='ttz';
system("cmd /c echo xx >$file");
# In our application, this file is created by a process
# on Unix. That's why we read it with the Unix layer.
# We do NOT set the layer during the open call.
my $layer=':unix';
open(my $fh,$file) or die "open error $!";
# In our application, a different function is responsible
# for setting the layer. Therefore, we use binmode to set
# it. Nothing had been read from the file so far, so this
# should be fine.
binmode($fh,$layer);
# Now close the file ...
close($fh) or die "close error $!";
# ... and try to delete it.
if(!unlink($file)) { # this is line 19
  warn $!;
  system("cmd /c del $file");
}
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Permission denied at fcstest1.pl line 19.
I:\tmp\ttx
The process cannot access the file because it is being used by another
+ process.
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