I find the easiest way to do this is to mark the closing tags with a unique character - I usually use an asterisk, but it can be any other character that doesn't exist in the rest of the file.

$lines =~ s/(<\/a>)/\*$1/gms;
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Then I search for two open tags without that character between them.

$lines =~ /<a[^\*]*<a/gms;
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