Several online commenters have pointed out that there are loopholes in WhatsApp’s end-to-end encryption guarantees. These include certain types of data that are explicitly shared with WhatsApp, such as business communications (when you WhatsApp chat with a company, for example.) In fairness, both WhatsApp and the lawsuit are very clear about these exceptions. These exceptions are real and important. WhatsApp’s encryption protects the content of your messages, it does not necessarily protect information about who you’re talking to, when messages were sent, and how your social graph is structured. WhatsApp’s own privacy materials talk about how personal message content is protected while other categories of data exist.
The lawsuit is not about metadata, or WhatsApp use within a company which is not E2EE apparently (making it very unsuited for work situations I'd say)