The main property of a reference field in D8 is still the target id:

$node->field_code_used_by->target_id = $user_id;

The entity property is a computed value. If you put an object in this value, drupal will convert it back to the id before saving it to the dababase.

Like in D7 the main property of a reference field in D8 is still the target id:

$node->field_code_used_by->target_id = $user_id;

The entity property is a computed value. If you put an object in this value, drupal will convert it back to the id before saving it to the dababase.

Multivalue fields

Add an item to a multivalue field:

$node->field_code_used_by[] = ['target_id' => $user_id];

The property target_id is not necessary, because it is the main property and used by default. So for most fields you can add a value like in a simple php array, which is easy to remember:

$node->field_code_used_by[] = $user_id;