We show that citation metrics of journal articles in many of the online-only Springer Nature journals and associated ones are distorted, going back to articles from 2001. We find that most likely due to an API response error, there are many incorrect references which typically lead to Article Number 1 of a given Volume. Among others, the issue affects journals such as Scientific Reports, Nature Communications, Communications journals, Cell Death & Disease, Light: Science & Applications, as well as many BMC, Discovery and npj journals. Beyond the negative effect of introducing incorrect reference information, this distorts the citation statistics of articles in these journals, with a few articles being massively over-cited compared to their peers, while many lose citations; e.g. both in Scientific Reports and in Nature Communications, 5 of the 10 top cited articles have article numbers of 1. We validate the distorted statistics by assessing data from multiple scientific literature databases: Crossref, OpenCitations, Semantic Scholar, and the journals' websites. The issue primarily arises from the inconsistent transition from page-based referencing of articles to article number-based referencing, as well as the improper handling of the change in the publisher's article metadata API. It seems that the most pressing problem has been present since approximately 2011, which we estimate affects the citation count of millions of authors.