This works without a warning

sub evalRna {
    my ( $left, $right ) = @_;
    my %bonds    = ( GU => 1, UG => 1, AU => 2, UA => 2, CG => 3, GC =
+> 3 );
    my $numBonds = $bonds{ $bases[$left] . $bases[$right] };
    my $level    = 0;
    my $new_left = $left;
    my $numRna;
    for ( my $i = $left + 1 ; $i <= $right ; $i++ ) {
        $level-- if ( $structure[$i] eq ')' );
        if ( $level == 0 ) {
            if ( $structure[$i] eq ')' ) {
                if ( $numRna = evalRna( $new_left, $i ) ) {
                    $numBonds += $numRna;
                }
            }
            $new_left = $i;
        }
        $level++ if ( $structure[$i] eq '(' );
    }
    return $numBonds;
}
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As you can see, I made some changes for better reading experience. The only change needed is to check if evalRna() returns undef. This caused your warnings. Maybe the return value undef is not, what your intention was.