local $/ = "Startpoint"; $temp="abc";
 while(<INFILE1>){ 

 /[(](\w+)[^(]+[(](\w+)[^:]+:\s+(\w+).*?slack[^-]+(-\S+)/s; 
       
 $PG{$3}{"$1-$2"}{"$cou"} = $4; 
 $cou++;
 }
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The first time you read the record that ends in  "Startpoint" there is nothing in the body of the record (at least, as far as I can see from the posted data). You then parse that data with a regex and add data to the hash regardless of whether or not the parse was valid. Try a modification like (untested):

my %PG;
my $cou = 0;

local $/ = 'Startpoint';
RECORD:
while (<INFILE1>) { 

    next RECORD unless  # unless valid data extracted from record
        /[(](\w+)[^(]+[(](\w+)[^:]+:\s+(\w+).*?slack[^-]+(-\S+)/s; 
       
    $PG{$3}{"$1-$2"}{$cou} = $4; 
    $cou++;
    
    }
[download]

It would also be wise to check the success of the open statement and die on failure.

Update: To answer your specific question: When the regex fails to match on the first (malformed) record,  $1 $2 $3 $4 are all undefined, as is $cou. The undefined value stringifies as  '' (the empty string), so you get a hash element of

--------------undefined key of my hash---------------
  '' => {
                   '-' => {
                            '' => undef
                          }
                 },
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