Faize's ending is by far the hardest, requiring these eight specific actions be done or it will be lost:
1. On the third leg of the flight from Lemuris to Cardianon, view Faize's first training event in the storage area north of the meeting room.
2. On the fifth leg of the flight from the Cardianon Mothership to the alternate Earth, trigger the event at the Item Creation terminal that ends with an accidental kiss between Lymle and Faize.
3. On the sixth leg of the flight from the Cardianon Mothership to the alternate Earth, speak with Lymle in the recreation room.
4. On the third leg of the flight from Planet Roak to Planet Aeos, skip the Meracle event and speak to Lymle in the recreation room instead.
5. Make Faize and Lymle roommates, then make sure to speak with them in their room during the fourth leg of the flight from Roak to Aeos, or after triggering the Faize training event while docked on Aeos.
6. On the second leg of the flight from Aeos to En II, have some cookies with Lymle and Faize in the recreation room.
7. On the seventh leg of the flight from Aeos to En II, speak to Sarah and Lymle in the room with the battle simulator.
8. While docked on Nox Obscurus, speak with Lymle in the storage area north of the meeting room. This one requires a lot of affinity between Lymle, Faize and Edge (but by doing the first 7 steps you should be there).
Crowe's ending is the second hardest, requiring these four specific PA's be done AND you must earn the endings for Reimi, Meracle and Sarah or it will be lost:
1. On the fifth leg of the flight to Cardianon, speak to Reimi in the room with the battle simulator.
2. After recruiting Myuria but BEFORE completing the Purgatorium, return to the Calnas to speak with Myuria and Bacchus in the crew quarters.
3. Either during the flight to En II or while docked there, trigger an event with Arumat and Reimi. Make sure to answer that Crowe is either your best friend or your enemy.
4. Place a funeral bouquet near the remains of Crowe's ship in the Halls of Termination on Nox Obscurus.