Off the top of my head, the likely issues are:
Untreated mental health issues, because a full MH assessment has not been made, and other treatments/therapies have been sidelined because transition has been assumed to be a cure all - sadly, this may not be the case, so increased risk of self-harm, harmful behaviours etc
Osteoporosis leading to fractures and reduced mobility
Infection risk from operations
Risk of death from complications of general anaesthetic
Females put on testosterone may end up with an increased risk of heart disease
There will be others. If you have a body which from a few weeks after conception is expecting high levels of one hormone, or a combination of hormones, and it suddenly doesn't get that, surely there are going to be issues. Your body will be fighting the drugs trying to suppress production of those hormones and the sudden rise in other hormones which your chromosomal makeup means your body is not expecting.