Seems this is catching a lot of people out. I'll try and add something that makes it clearer, but for now here are the criteria you need to take into account when choosing a song/mode for a Shadow Mission.
Note 1: Tracks with the Shadow Ops Icon can be used to complete the current mission
Note 2: Choosing 'Play Random Track' or 'One I've not played yet' will automatically choose a song that will meet the current mission criteria.
Mission Restrictions
Shadow Missions have some restrictions. These are listed below.
In general, songs with the Shadow Ops Icon next to them are appropriate for the mission.
Destroy 'x' small ships of type 'y'
Any mode. Tracks with Icon present
Destroy 'x' big ships of type 'y'
Any mode. Tracks with Icon present
Destroy 'x' bosses of type 'y'
Any mode. Tracks with Icon present
Score 'x' points in 1 track
Standard Mode Only
Accumulate 'x' points
Standard Mode Only
Complete 'x' tracks on 'y' difficulty
Standard Mode Only
The track must be longer than 3m:30s
You can play on higher difficulty if you wish
Collect 'x' pickups of type 'y'
Any mode. Any track
Death Penalties
If you die during a shadow mission, you will lose some of your progress in that mission. Below are the types of mission and their penalties:
Destroy 'x' small ships of type 'y'
100% Progress Lost
Destroy 'x' big ships of type 'y'
Lose 2 Kills
Destroy 'x' bosses of type 'y'
Lose 1 Kill
Score 'x' points in 1 track
100% Progress Lost
Accumulate 'x' points
Lose 1 million points
Complete 'x' tracks on 'y' difficulty
Lose Current Track
Collect 'x' pickups of type 'y'
10% Progress Lost