I'd say it doesn't so much contradict the existing science as it suggests the possibility that the population-level correlations we see are not explained by direct effects of social media use on individuals.
Just as an illustrative example, suppose Alice has an higher-than-average need for in-person social interaction in order to remain mentally healthy, and so has decided not to use social media. If the people around Alice start spending more than some critical percentage of time on social media instead of in-person socializing, then her mental health might decline even though she doesn't use social media.
I have found articles linking social media to worse sleep quality (and sleep quality and depression are well known to influence each other) but still no direct link.
Do you happen to know what papers prove the link between depression and social media use in children? The theory makes sense but I can't find studies that prove more than mete correlation.
This is not the average case scenario as the majority of children on social media and the longest amount of screen use are of children who are often not in after school programs or daycares. The reality is that this study is not a good measure of if social media causes depression or not.