According to WhatsApp, it seems that lost messages are one of the reasons why the company has decided to ban third-party apps. A portion of the statement reads, “Third parties that have built unauthorized functionality on top of WhatsApp create issues for people including lost messages. This goes against the experience we work hard to give people and we won’t let it continue.”
However it is possible that issues like last year’s The Snappening could have prompted WhatsApp’s stricter stance on third-party clients. For those who missed out on last year’s news, The Snappening was when photos taken by Snapchat users were leaked online. This wasn’t due to Snapchat’s servers being compromised, but rather the third-party’s service.
Since WhatsApp, just like Snapchat, has no control over how developers program their apps, it would basically be out of their control when something goes wrong. The third-party WhatsApp client WhatsApp+ has since been officially killed off after receiving a cease and desist letter from the developers.