Shay Act 1
While this trophy is based on an unmissable storyline event, it is perfectly possible not to complete this puzzle flawlessly, therefore the trophy itself is missable. It is, in my opinion, the hardest trophy of the game.
There are three rescue missions where Shay must rescue creatures from the universe in a mini-game that reminds me of those crane machines that you would find in any decent seaside arcade. You cannot miss at any time -- you must pick up each creature on your first attempt. These videos show all three rescues performed flawlessly.
First mission: After talking to Marek for the first time, you are given a Star Chart for the Talon Nebula. Take the Star Chart to the Space Weaver and he will transport the ship to the Talon Nebula. Create a MANUAL SAVE here. If you miss the two creatures on your first attempt, you can reload this save.
Second mission: Immediately after the first two creatures, you must go on another mission to Danger System 5. Take the new Star Chart to the Space Weaver. After he has transported the ship to Danger System 5, create a MANUAL SAVE again. There are five creatures in this mission. If you miss any of these creatures on your first attempt, you can reload this save again.
The third mission requires you to travel to Prima Doom. Before you can do this, you must regain control of the Boom Arms, place the Inhibitor on the Fusion Orb and force the Space Weaver to take the ship to Prima Doom. I advise that the last activity that you complete is to take the ship to Prima Doom. Once the Star Weaver has shut down, make a MANUAL SAVE. If you have to reload this save, there is minimal distance to travel to get back to Marek's room.
In the third mission, there are three creatures to rescue. Both the Boom Arm and the creatures are moving fairly quickly, so the chances are that you will need to reload your manual save. If you manage to rescue the first creature on your first attempt, make a MANUAL SAVE so that you don't have to retrace your steps to get back to the controls. While you will have to rescue all three creatures again, the game will still think that you rescued all of them on your first attempt and will award you with the trophy.
If you have to reload a manual save, DO NOT enable Auto-Save as this will overwrite your file. However, if you are successful after reloading a save, you will need to make manual saves from that point onwards because Auto-Save has been disabled.