A completely different approach that turns out to be far simpler and more robust. (Ie. It actually works for all possibilities:)

In addition, it avoids a bunch of convoluted range comparisons and the need for sorting, whilst producing fully sorted output. A win-win-win for going back to the drawing board.

#! perl -slw
use strict;
use Data::Dump qw[ pp ];

sub dhm2int {
    my( $d, $h, $m ) = unpack '(A2)*', $_[0];
    return ( ( $d - 1 ) * 24 + $h ) * 60 + $m;
}

sub int2dhm {
    sprintf "%02d%02d%02d", int($_[0]/1440)+1, int($_[0]/60)%24, $_[0]
+%60;
}

#my @listone = 
    (['010000','010010',2],['010200','010210',5],['012359','020001',3]
+);
#my @listtwo = 
    (['010005','010015',1],['010207','010211',4]);
my @listone = 
    (['010000','010110',6],['010200','010210',5],['012350','020012',3]
+);
my @listtwo = 
    (['010005','010015',1],['010207','010211',4],['012355','020003',1]
+);

my @expd = map {
    my $in = $_;
    my $s = dhm2int( $in->[ 0 ] );
    my $e = dhm2int( $in->[ 1 ] );
    my @out;
    while( int( $s / 1440 ) != int( $e / 1440 ) ) {
        my $newe = ( int( $s / 1440 ) +1 ) * 1440 -1;
        push @out, [ int2dhm( $s ), int2dhm( $newe ), $in->[2], $s, $n
+ewe ];
        $s = $newe +1;
    }
    ( @out, [ int2dhm( $s ), $in->[1], $in->[2], $s, $e ] );
} @listone, @listtwo;

my( @tally, @id ); 
for my $e ( 0 .. $#expd ) {
    my $r = $expd[ $e ];
    for my $i ( $r->[ 3 ] .. $r->[ 4 ] ) {
        if( !defined( $tally[ $i ] ) or $tally[ $i ] > $r->[ 2 ] ) {
            $tally[ $i ] = $r->[ 2 ];
            $id[ $i ] = $e;
        }
    }
}

my @res;
my $i = 0;
while( $i < $#id ) {
    ++$i until defined $id[ $i ];
    my $id = $id[ $i ];
    my $start = $i;
    ++$i while defined( $id[ $i ] ) and $id[ $i ] == $id;
    my $end = $i - 1;
    push @res, [ int2dhm( $start ), int2dhm( $end ), $tally[ $start ] 
+];
}

pp \@res;

__END__
C:\test>935755.pl
[
  ["010000", "010004", 2],
  ["010005", "010015", 1],
  ["010200", "010206", 5],
  ["010207", "010211", 4],
  ["012359", "012359", 3],
  ["020000", "020001", 3],
]


C:\test>935755.pl
[
  ["010000", "010004", 2],
  ["010005", "010015", 1],
  ["010200", "010206", 5],
  ["010207", "010211", 4],
  ["012359", "012359", 3],
  ["020000", "020001", 3],
]
[download]