Somatic genome diversity can be an important factor in human disease, including age-associated pathologies such as cancer. Overcoming challenges particularly associated with the detection of somatic DNA variants is now poised to become crucial, considering efforts to include them in precision medicine-based healthcare models. The nanopore sequencing approach of Oxford Nanopore Technologies (ONT) is likely to become an important player in this space due to its ability to yield results in real time without PCR, suitability for adaptive sequencing, ability to resolve structural variants, and capacity to resolve DNA base modifications. A key consideration here is that whilst ONT sequencing may be PCR-free, we find it is not artefact free. After mixing DNA from human, macaque and mouse and advancing through PCR-free ligation-based ONT library preparation, we found numerous reads composed of regions derived from the DNA of different species. These data were generated both in-house and in a dedicated sequencing facility, and using multiple library preparation kits and ONT sequencing platforms. We conclude that ligation artefacts are generated using standard library preparation protocols. Such artefacts necessitate additional filters and read count thresholds to reliably call genuine somatic recombination events.