Concerned with large scars after FUE transplant 36 days post-op. Any ideas why this is happening? (Photo)

I would talk to your doctor. This could be shock loss, which would recover on its own within a few more months. Could also be overharvesting, which will not recover on its own but you could mitigate with scalp micropigmentation or other methods. It could also be something else entirely, its hard to make an accurate guess over the internet.

healing on the donor area takes sometimes more time (body support,the size of punches,the type of punch (sharp or not ) for extraxt the hair follicules,and of course the experience.

Dont worry it will looks much better after 2-3 month period.İts early to say if its over harvesting or not!Update your pictures.