In season 9 episode 14, a dog is thought to be killed but was really kidnapped. Overall this episode is pretty pro-dog and the dog was fine in the end. the dogs in this episode are adorable actually. It's also one of the few episodes where no one is actually hurt. The kidnapper's motivation is that he needs money to feed his own dogs. Everyone in this episode loves doggies.
A dog is also injured in an early episode of the show, but it gets better.
In the first episode: The female character (minor) physically assaults the male character (also a minor). She kicks him in a way that he ends up with his head under her skirt. It was completely unnecessary to add this scene.
Rachel is gaslit constantly by Jimmy/Conan in order to maintain his secret identity. This includes convincing her that she's delusional and fabricating fake evidence to support his lies
Although Conan isn't truly a child, Kogoro is shown hitting him, shouting at him, and otherwise neglecting him. Child abuse is also mentioned in several cases.
Episode 138-139, 159-160, 222-224, 315, 397, off the top of my head. A synopsis and cause of death for each episode is listed on the wiki if you're unsure.
• When Miwako was a little girl, her father get involved in a traffic accident and died, such event marks a lot her life; • In the past, Jodie's parents were killed by Vermouth, when that happened Jodie was only a child;
• In Kir Arc's is shown that Ethan Hondou, Hidemi father, commits suicide to protect his daughter;
In the filler episode, The Kidnapper in The Picture" the kidnapper is dressed up as a clown. Also in "The Wizard of the Ripples" is mentioned and shown clowns in the background;
The 5th movie "Tengoku no countdown" makes a lot of references to 9/11 because of the twin towers but there's no aeroplanes involved in this and -SPOILERS: everyone except conan and their friends are evacuted, they get to scape and the tower doesn't colapse-
A character, Eisuke Hondou, is established to have had leukemia as a part of his backstory. However, the leukemia was treated some time prior to the start of the series and Eisuke has been clear of it for years.
Several one off characters in various cases are established to have died of cancer or to have cancer.
Shinichi and Shiho survive a poison, but are deaged into children as a result. They age back and forth between children and their teenaged selves via temporary antidotes to the poison, and while the process isn't graphically shown in the manga (A few anime episodes do show Shiho shrinking into her child self), it is established to be extremely painful. This is the driving plot point and can't easily be ignored.
In the German version of The Disappearing Detective Boys Case (E176 internationally), the word is used several times as part of the title of Agatha Christie's And Then There Were None.
In The Moonlight Sonata Murder Case, a character presenting as female is revealed to be assigned male at birth- and are referred to as male after the reveal. Whatever their true gender identity actually is, they're being misgendered at some point throughout the plot.
A dog is also injured in an early episode of the show, but it gets better.