A quick peek at the plot on the wikipedia, combined with my faltering memory, seems to point out at the scene on the roof(?) with Mr.Junkers being shot by Johan. The kid just killed two men(Junkers&guard at the door), and Tenma just lets him go(because he apparently couldn't kill somebody he saved once, even though that somebody just proved beyond any doubt to be a homicidal maniac). He does not tell the police that there's a juvenile murderer on a shooting spree, instead he lets the detective put all the (suspected)blame on himself.
Why he does not work with the police? There's enough evidence to at least warrant finding and questioning Johan. There's the twin sister who has been talking about disturbing stuff earlier, why not question her? There have been people getting killed, and people in danger of being killed(the twin sister), yet he decides that it's better idea to have the police against him, hide get a gun, and take marksmanship lessons. Is he daft or what?
Why did nobody try to apprehend Johan after the previous murdering spree in the hospital? He was like, the only person missing afterwards, that should at least warrant if not questioning, then concern for his wellbeing and whereabouts. Why was there no investigation for the case of those kids? Did nobody look for a reason why the kid had been shot in a head? No weapon found?(did the sister hide it after shooting her brother?) Nobody seemed to care about first having a kid with a headwound, and later on, having him dissapear.
Also, you've mentioned it being the realistic depiction of life in '90s Germany - what about people acting as if they were all Japanese, like e.g. thanking each other with that characteristic Japanese bow?
ed:some bad grammar etc.