The association handling in DomainObjectMerger is in place to allow the creation of resources using PUT that have non-optional associations. However, if the domain types that the request payload was unmarshalled into use default values - in particular empty collections to avoid nulls - the merger cannot really distinguish between the default set in the type versus an empty collection being submitted through the request.
As the usecase here is creation only we can safely ignore empty collections as submitting those doesn't make a difference anyway (no related items attached). By ignoring those, we fix the issue defaulted empty collections in the type definitions being considered as value to set.