In all but the first iteration, the last regexp isn't matched, resulting in a repeat of the article title. (I guess that the backreference from the regexp to capture the article title is assigned to $source_journal, which is then printed)

Captures like $1 are only valid if a regex actually matched...  So the solution would be to test if it matched, and assign some other (default) value to $source_journal in case it didn't.

if ($new_url =~ m{(...)}) {
    $source_journal = $1;
} else {
    $source_journal = '(not specified)';
}
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