Ridden entities get saved seperate causes them to unmount when reloaded

Explosions have a chance of droping tnt while still igniting it

Boats always get placed in the same directon and not based on how they get placed

Swords with fire aspect deal damage before setting the target on fire, thus leading to raw meat

Burning arrows can't ignite tnt when they hit it at the top

Enderpearls (and other throwable objects) loose their link to the thrower when reloaded

Lightning strikes create clientsided (phantom/ghost) fire. The client shouldn't be allowed to create this fire.

The hitbox of ladders don't update by just looking at them

Netherportals create a huge lag, especially when serveral entities have to be teleported

Mobs can pick up items on their death and destroy them that way (including their own drops)