When I run your code, I get a quite different set of results from those you posted.

P:\test>test
 Xq27-q28
 22q12.1
 19q
 1q25
 11p11.2
 10q23.31
 8p22
 7p22
 19q12-q13.11
 52
 15
 19q12-
[download]

Which makes it difficult to try and answer your two questions.

In any case, it is probably better to specify the regex more accurately so that you don't capture the unwanted values in the first place. This seems to do the trick on the sample you supplied.

#! perl -w
use strict;

my $text = <DATA>;

my $re_1chrom = '[\dXY]*[pq]\d+(?:.\d+)?';
my $re = qr[\b$re_1chrom(?:-$re_1chrom)?\b]i;
my @chroms = ( $text =~ /$re/g );
print $_, $/ for @chroms
__END__
P:\test>test
Xq27-q28
Xq11-q12
22q12.1
1q42.2-q43
17p11
1q25
13q12.3
11p11.2
10q25
10q23.31
8p22
8p22
7q11.23
7p22
19q12-q13.11
19q12-q13.11
[download]

The sequential double reference to 8p22 seems odd in context, but eliminating that and the other duplicate(s) is a simple step.