"\1" means the first opened parenthesis. You need to use "\2".

$ perl -e '$_="aaabbccccddeee"; print $1,$/ while /((.)\2*)/g'
#                                                  ^^
#                                                  ||
#                                                  |+--- \2
#                                                  |
#                                                  \1
aaa
bb
cccc
dd
eee
[download]

Or, if you want an array as a result,

 push @array, $1 while  /((.)\2*)/g;
[download]

Update
Notice that you can't just assign the outcome of the regex to an array, because you'd get redundant results (both $1 and $2 for each match).

# THIS IS WRONG
@array = $_ =~ /((.)\2*)/g;
print join ", " , map {"<$_>"} @array;
__END__
<aaa>, <a>, <bb>, <b>, <cccc>, <c>, <dd>, <d>, <eee>, <e>
[download]

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