The TLDR is that there are several issues with the study methods which are apparent from available materials (and probably even more apparent from the actual study data which has been withheld by the authors). The cohort that received gender affirming care over the twelve months showed no improvement over baseline, while the control cohort deteriorated into even higher levels of depression/anxiety/suicidality. Instead of looking at the treatment group and saying "there has been no improvement", they compared it to the control and said "they haven't deteriorated like these people have."

Unfortunately, the vast majority of the control cohort simply stopped responding to the survey over 12 months, so there is no end to potential confounding factors causing children (who for all we know elected not to receive gender affirming care to begin with) to stop responding to a survey issued by a gender clinic, or the confounding factors that caused the others not receiving treatment to remain in the study.