SPOILERS: Most of the animals in the zoo die on screen or disappear between scenes. Once the violence starts, an elephant is shot, a baby camel is shot, a bald eagle is shot, the skunk survives, and many other animals are shown as carcasses after the bombing.
A girl is raped but the act itself is not shown.
Antonina is sexually harassed throughout the movie and eventually the Nazi sexually assaults her. It doesn't go to the point of rape/penetration.
The burning of the Warsaw ghetto is depicted and screaming can be heard. In another scene, battle in the Warsaw streets is depicted, during which some people burn.
Not on-screen, but plenty of Jewish children are shown to be put on a train to concentration camps. Also, there is a distressing scene where a child gets taken off-screen with a gun pointed at him, and a gunshot goes off. Spoilers, I guess: He isn't shot, however.