Yield maps are recognized as a valuable tool with regard to managing upcoming crop production but can contain a large amount of defective data that might result in misleading decisions. These anomalies must be removed before further processing to ensure the quality of future decisions. This paper proposes a new holistic methodology to filter out defective observations likely to be present in yield datasets. The notion of spatial neighbourhood has been refined to embrace the specific characteristics of such on-the-go vehicle based datasets. Observations are compared with their newly-defined spatial neighbourhood and the most abnormal ones are classified as defective observations based on a density-based clustering algorithm. The approach was conceived to be as non-parametric and automated as far as possible to pre-process a growing number of datasets without supervision. The proposed approach showed promising results on real yield datasets with the detection of well-known sources of errors such as filling and emptying times, speed changes and non-fully used cutting bar.