To be able to tag loose crates in the environment you need an untasked cargo ship in your squad. The Albion Skunk AI will tell you don't have a cargo ship available when you try to select cargo view mode: <enter>, 1, 2 with no untasked cargo ship in your squad.
The cargo ship will need to be equipped with Cargolifter URVs to collect the tagged crates.
Once in the cargo mode you will not be able to tag crate types that you don't have a ship of the correct type: liquid, energy, container, bulk etc.
Bug: Occassionally the tagging system will allow you to tag any crate regardless of the ship/crate type mismatch.
In cargo mode if you leftclick to select a taggable crate and then "f" to tag. When you do tag a crate it will be outlined in white. Once tagged the cargo ship will send Cargolifter URVs to collect the crates.
Bug: If you set the cargo ship to trade some of these collected crates, any uncollected crates will remain tagged but will not be collectible at any later time. These un-collectible tagged crates will be visible in the sector map turning that sector green to indicate your property in the sector.