Note that you have two very similar statements in the OPed code that are doing very different things:

my %lag_detail = ...;  # single instance of this hash in scope
...
foreach my $line (...) ) {
    if (...) {
        if (...) ) {
            # push ref. to OLD instance of a hash to anon. array in an
+other hash.
            push( @{ $self->{"lags"} }, \%lag_detail );
        }
        # change certain values in hash, but hash LOCATION does not ch
+ange.
        %lag_detail = ( "lagid" => $lag, "lagdesc" => $4, "operationst
+ate" => $3, "adminstate" => $2 );
    }
}

if (...) {
    # create NEW instance of a hash in independent scope.
    # this instance is TOTALLY INDEPENDENT of any other created in thi
+s scope.
    my %port_detail = (...);
    # push ref. to NEW instance to anon. array in another hash.
    push @{ $lag_detail{"ports"} }, \%port_detail;
}
}
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