What Anonymous Monk said:

while (my ($match) = m/$regex/g) {
    $matched{$match} = 1;
    print "$file $_";
}
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gives you an infinite loop.

c:\@Work\Perl\monks>perl -wMstrict -le
"my $regex = qr{ \b f[eio]e \b }xms;
 ;;
 $_ = 'xx fee fie foe yy';
 while (m/($regex)/g) {
   my $match = $1;
   print qq{captured '$match'};
   }
"
captured 'fee'
captured 'fie'
captured 'foe'
[download]

works better (at least it stops). If you want to get a bit fancy,

while (m/($regex)/g and my $match = $1) {
  print qq{captured '$match'};
  }
[download]

also works. But the whole "extract multiple matches per line" thing may not even be a real issue! The OPer says nothing about it, and I only raised it as a cautionary point of interest.