$inputfile1 =~ s/\s*\z//;

$inputfile1 is your filehandle, but you are editing that filehandle and thus corrupting it. Try:

sub mainCSV {
    open (my $inputfile1, '<', "$inputfile") or die "Unable to open $i
+nputfile1: $!";

    my %hash;

    while( my $line = <$inputfile1> ) {
        $line =~ s/\s*\z//;
        my @arrayfile1 = split /,/, $line;
        my $keyfile1 = shift @arrayfile1;
        $hash{$keyfile1} = \@arrayfile1;
    }

    print %hash;
    close $inputfile1;
}
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