Do i need to manually loot drops from enemies / crates?

Some items are granted at the end of every mission, but im not sure if system checking whats inside crates.

Do i need to open every one of them inside mission to get goodies or they are automatically added as loot at end of each scenario?

Same with drops from mobs - do i need to manually pick them up to get them?

In Haven defence missions you need to pick items from the ground and you need to open crate to get it’s content at the end of the mission. In other missions you don’t need to do that.