You push $1 onto @array (push (@array, $1);) regardless of getting a match in the previous regex. Unless the last matching line in your file is a well formed $lastPhrase line, your code as it stands will fail as you have noted.

The following test code illustrates the problem:

use strict;
use warnings;

use List::Util qw{first};

my $file = <<FILE;
total rejected recors: 10
FILE
my @phrases = (
    "total rejected rows:",
    "total rejected recors:",
    "rejectb:",
    "total rejected rows:"
    );

open my $inFile, '<', \$file;
my @newarray = search_phrase ($inFile, @phrases);
close $inFile or die qq{close: $!\n};

$newarray[$#newarray] =~ s/\s+//g;

if (@newarray && $newarray[$#newarray] > 0) {
    print "$newarray[$#newarray]\n";
} else {
    print "-1\n";
}


sub search_phrase {
    my ($inFile, @phrases) = @_;
    my @array;
    my $lastPhrase = $phrases[-1];
    my @lines = <$inFile>;

    foreach my $phrase (@phrases) {
        # Find the first match in the remaining lines for the current 
+phrase
        my $lineNo = first { $lines[$_] =~ /\Q$phrase\E/ } 0 .. $#line
+s;

        next unless defined $lineNo; # No line containing current phra
+se

        print "Found: $lines[$lineNo]"
            if ($lines[$lineNo] =~ m{\Q$lastPhrase\E\s*(\d+)});

        push (@array, $1);
        $lineNo++;
        splice @lines, 0, $lineNo; # Delete processed lines
    }

    return @array;
}
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