Special events can occur within the Bathhouse of the castle after collecting and decorating it with antiques. One of the special scenes happens after setting 6 Chinese Plates, where two party members, Wakaba and Long Chan Chan, drop from above for undisclosed reasons; They sometimes appear on the side opposite to their gender.

During an interview, it was revealed that the game's illustrator, Fumi Ishikawa, was a big fan of Flik. The team created a fake set of planning notes for Nina's unite attack with Flik in case Ishikawa was to delete it out of anger for Nina and Flik's relationship.

In a developer interview published in the March 1999 issue of DenGeki PlayStation magazine, it was revealed that Rowd, a character who betrayed the Unicorn Youth Brigade of the Highland Kingdom, was the older brother of the little blind girl in Kyaro Town who disappears near the end of the game, and his motivation for his betrayal was to save more money to cure her blindless. When talking to the girl in Kyaro Town, she states that her big brother plans to use his riches to hire a famous doctor in the Toran Republic (who is suspected to be Liukan, a character from Suikoden who briefly appears in this game) to perform the operation. During the interview, programmer Akiyoshi Ohta also stated that there was originally going to be a battle against Rowd where he would die, but this was cut because "his little sister was too cute to do it."

In Banner Village, the side quest to recruit Tir McDohl is affected if the game imports save data from Suikoden. If the player imports a save file with the 108 Stars of Destiny recruited in the first game, Gremio will appear in the game starting with this side quest. However, in a developer interview published in the March 1999 issue of DenGeki PlayStation magazine, director Yoshitaka Murayama revealed that should you import a save file without recruiting all 108 Stars of Destiny, Ellie will replace Gremio in the Banner Village events of the side quest.

According to Suikosource user JiN88, the Japanese demo of Suikoden II contains two debug/testing rooms.

The first test room claims to be in Radat Town, despite seeming to be in Kyaro Town. The room contains various warping and unfinished textures, out-of-place objects like barrels, and two non-functioning Warp points. Of the warp points, one can be found down near a river and loads nothing, while the other can be found near a bridge with an Anita NPC and some invisible objects. While this test room seems to be empty, except for one small area featuring several invisible objects, a pushable tree that you can talk to, and a row of NPCs that can be pushed, but cannot be interacted with without crashing the game. There are also two Gabocha NPCs, one of which can warp you back to somewhere else in the test room, while the other has some dialogue and acts like a shopkeeper. Finishing the conversation with the shopkeeper Gabocha will cause the game to crash. Interacting with any Anita NPC will cause the game to crash.

The second test room contains several repeating groups of Anita, Gengen, and Old Man NPCs in a sort of army formation. The name of this second debug room is "神様の村" which means "Village of God"/"God's village". Talking to the Anita and Gengen NPC groups will have them say a single line of dialogue (the Anitas however will have no text), and once finished will cause the game to try and load something, which results in the game crashing. It's thought that they would try to warp you somewhere with a cutscene. Raww Le Klueze, global admin of the Suikosource forums, has translated this room's dialogue as such:


This latter piece of dialogue might be a reference to the song "Nice Hot Water", a 1966 song in the "Nihon no Uta" Japanese local song series that was famously covered by the Japanese comedy rock band The Drifters. The first line before the hyphen is the same as the song, and the second line after the hyphen is almost the same as the song.