You might find Data::Dumper helpful. Try adding the following to the end of your script:

use Data::Dumper;    # you could put this at start of script

print Dumper(\@all_matches);
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This will print your data structure in a fairly easy to understand format (see the documentation for details). It might help you to find and understand what is undefined.

This was very helpful! I will use it to debug from now on! ...After I read all it can do. Thanks!

             if ($line =~ /^Parsing \[(sent. \d+) len. \d+\]: \[(.+)\]
+/) {
                 #$one_match_ref->[1] = $1; ##Multiple in file
                 #$one_match_ref->[2] = $2;
                 #$one_match_ref->[2] =~ s/,//g;
                 my $nocomma_sent = $2;
                 $nocomma_sent =~ s/,//g;
                 push( @{$one_match_ref}, $1, $nocomma_sent);
             }
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This might be the source of one of your uninitialized values.

See perlre for details of the match variables ($1, $2, etc.). The important thing here is that these variables are reset by the next successful match. If your substitution to remove commas finds any, then it is a successful match, after which $1 and $2 are reset to undef. Thus, if $nocomma_sent has any commas in it, when you push $1 onto your array you will be pushing undef.

One way to avoid this is to push $1 before performing the substituion:

             if ($line =~ /^Parsing \[(sent. \d+) len. \d+\]: \[(.+)\]
+/) {
                 push( @{$one_match_ref}, $1);
                 my $nocomma_sent = $2;
                 $nocomma_sent =~ s/,//g;
                 push( @{$one_match_ref}, $nocomma_sent);
             }
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That did the trick! Thanks a lot! (Too bad I have to restructure this method... still I won't make the same mistake!)

By the way, don't you mean if it _doesn't_ have any commas in it?

One thing you will get good at is testing your ideas. Sometimes reading the documentation or posts here give you ideas, but you will not be certain about them until you try them. Try this:

use strict;
use warnings;

my $text = 'axa bxb cxc dxd';

print "1 - \$1 = $1, \$2 = $2\n";

$text =~ m/(a\w*) (b\w*)/;

print "2 - \$1 = $1, \$2 = $2\n";

my $x = $2;

print "3 - \$1 = $1, \$2 = $2\n";

$x =~ s/,//g;

print "4 - \$1 = $1, \$2 = $2\n";

$x =~ s/x//g;

print "5 - \$1 = $1, \$2 = $2\n";
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By the way, don't you mean if it _doesn't_ have any commas in it?

If the string had no commas, there would be no successful match in the regex 'search' phase of the substitution, and  $1 and  $2 and any other capture variables would not be undef-ed. See the substitution statement
    $x =~ s/x//g;
that is the second to the last statement in ig's example code in Re^5: Error: Use of uninitialized value $item in concatenation (.) or string at...: the successful match against  $x causes all capture variables to be set to the values of their corresponding capture groups, and since there are no capture groups, these values are all undef.