There're only two ways I know to avoid "spurious" capture groups in Perl 5.8.x regexes: don't use capture groups at all, or grep them away. Here's another approach that might or might not fit with your "... expressions [that] are much more complicated ..." in the pairs of regexes (update: tested under ActiveState 5.8.9):

c:\@Work\Perl>perl -wMstrict -MData::Dump -le
"print qq{Perl version: $] \n};
 ;;
 my $fc =
  'abcdfoofrobnicatebardefforspambazghixyproblemaaaxyzzylettuce';
 ;;
 my $min = qr{ .*? }xms;
 ;;
 my @groups = (
   [ qr{ fo. }xms, $min, qr{ ba. }xms, ],
   [ qr{ xy. }xms, $min, qr{ le. }xms, ],
   );
 ;;
 my ($find) =
   map  qr{ $_ }xms,
   join q{ | },
   map  qr{ @$_ }xms,
   @groups
   ;
 print qq{$find \n};
 ;;
 my ($capture) =
   map  qr{ $_ }xms,
   join q{ | },
   map  { map qr{ $_ }xms, join ' ', map qr{ ($_) }xms, @$_ }
   @groups
   ;
 print qq{$capture \n};
 ;;
 my @excerpts = $fc =~ m{ $find }xmsg;
 dd \@excerpts;
 ;;
 for my $exrpt (@excerpts) {
   my @parts = grep defined, $exrpt =~ m{ $capture }xmsg;
   printf qq{'$_' } for @parts;
   print '';
   }
"
Perl version: 5.008009

(?msx-i: (?msx-i: (?msx-i: fo. ) (?msx-i: .*? ) (?msx-i: ba. ) ) | (?m
+sx-i: (?msx-i: xy. ) (?msx-i: .*? ) (?msx-i: le. ) ) )

(?msx-i: (?msx-i: (?msx-i: ((?msx-i: fo. )) ) (?msx-i: ((?msx-i: .*? )
+) ) (?msx-i: ((?msx-i: ba. )) ) ) | (?msx-i: (?msx-i: ((?msx-i: xy. )
+) ) (?msx-i: ((?msx-i: .*? )) ) (?msx-i: ((?msx-i: le. )) ) ) )

["foofrobnicatebar", "forspambaz", "xyproblem", "xyzzylet"]

'foo' 'frobnicate' 'bar'
'for' 'spam' 'baz'
'xyp' 'rob' 'lem'
'xyz' 'zy' 'let'
[download]

(Please forgive the wrap-around in the long regex print statements. I've tried to mitigate the effects; I hope I didn't introduce any | too much cruft.)

Update: Of course, this is an attempt to generalize tye's approach above to deal with unlimited pairs of regexes. Whether it applies to your situation is a separate question.