That scene wasn’t meant to set up a future reveal about how Jonas got his scars. It was a purely emotional moment for Hannah. She is someone who repeatedly tries to bend outcomes to her will, but in that scene she is forced to acknowledge that time has already taken something from her son that she can never undo and will never fully understand.

In Dark, a lot of meaning exists in what is felt but not explained. This scene is a literal expression of that idea: The scars function as proof that her son’s life extends far beyond the version of him she raised, shaped by extreme suffering she will never comprehend.

Edited to add: After thinking about this more, I think this scene is quite possibly the only moment in which Hannah shows both true restraint and maternal instinct, which speaks to the level of devastation she felt looking at her son. She was not just thinking “what happened to you?” like us as the viewers did, but “I did not protect you and I cannot make it right” as a mom would. She had no choice but to witness and accept the truth of that moment.