[Mivereous]

After thinking more on it, there was a couple reasons why this happened. I will post all the things that might lead to this conclusion.

1) Have 5 youkai.
2) Unlock Bonder.
3) Equip Bonder.
4) Max Spiritual Bond (3 SP).
5) End contract with youkai until you only have 2.
6) Have one of the youkai's Friendship "above average" (Bonded), and the other one below average (non-Bonded).
7) End contract with the "Bonded" youkai.
8) The "non-Bonded" youkai is now only treated as Bonded when "above average" Friendship, and not since it is the only youkai in your list.



1) Have 5 youkai.
2) Unlock Bonder.
3) Equip Bonder.
4) Max Spiritual Bond.
5) Dismiss youkai until you only have 1.
6) This youkai (A) is now treated as always Bonded, as Spiritual Bond explains.
7) Grab another youkai (B). Highest Friendship youkai is now preferred for Skills, as Spiritual Bond explains.
8) End contract with youkai A.
9) Youkai B is now only treated as Bonded when "above average" Friendship, and not since it is the only youkai in your list.