End of Game Freeze
It is possible to have your game freeze as you finish fighting the Act II final boss. When this occurs, portraits will become glitched, and the game will freeze during the credits. You will have to hard reset, and progress you made since your last save will be lost.
Known Workarounds: Go to your settings and turn off portraits, BGM, SFX, and do not bring anyone with you to the final battle. This will greatly reduce your risk of encountering the glitch. Failing to do this does not guarantee you will encounter the glitch, but if your game freezes once then you should do this on your second attempt. This workaround is not a guarantee that the game won't freeze as the character models will instead glitch rather than the portraits. It is best to start over from the last save when encountering the glitch during the dialogue scenes as it is a sure indicator that the game will freeze during the credits.
At random, the game graphics may glitch. Portraits will usually become bugged first, followed by sprites and scenery. The exact triggers are unknown, but this is an uncommon bug.
Repeat Boss Battles
Although you get Prince Points/Princess Points and boss drops appear when a boss monster vanishes, the barrier around a boss room will linger for a second longer, and the game does not consider the boss battle completed until the barrier disappears. If you warp out of the room before this happens, you can fight a boss multiple times a day. 
In arc 1, as soon as Venti colapses, if you are married you can skip the three rune spheres before the heaven's gate battle by going to Leon Karnak solo. Once you pass the save station, the dialogue between you and your spouse will begin like it is supposed to as if you were at that point normally and married. The rune spheres are be active in the guardian rooms as if you progressed normally.
This is a good trick to use if stuck with an Iron Watering can and want to speed up the process of watering. Charge up the watering can and then as soon as you release the charge, rapidly press the B button while moving. This will water 2-3 spots at a time, however it will consume water as if you were continuously using the charge.
The game sometimes or frequently locks up during normal play. The most common culprit is using fully range-extended weapons that can inflict all status ailments on a large crowd of enemies.
Character portraits and occasionally other graphics will have blue lined bars running through them. Often occurs as a result of too much soft-resetting, and can generally be triggered on Beach Day by hanging around Dragon Lake all day long without leaving the screen.
During the Fishing Frenzy Contest, it is possible to come across a line where Margaret speaks in Japanese. All she says is Forte's name. One random traveler also has an untranslated line of dialogue.
If you throw a piece of furniture that is capable of storing items, then throw a storable item at it before it has finished bouncing, the furniture will float away. You can still interact with the furniture by inspecting the space where it is supposed to be, and if you leave the room and come back, the furniture will have returned.
Some field and barn names will revert to default upon reseting or reloading the game.
The Senility of Volkanon
He can abruptly begin referring to Frey as "Sir" rather than "Miss." By seeing the "Someone Has The Wrong Idea" event before getting married clears this glitch up.
Don't Do It!
Characters can sometimes be found standing in places such as on the palace roof, on top of furniture, or stuck in the cliff at Dragon Lake. You can also find NPCs like Barrett, who will appear to be outside the castle where your room will be, however he is off the map and unlocatable.
Dylas will sometimes display a sad portrait when he should be blushing. However, this does not appear to be as much a glitch as it is an oversight by the developers where Dylas does not have a blushing portrait in his bathing suit or pajamas.
Luna and Noel can abruptly start referring to Frey or Lest by their first name. They can also randomly address Frey as "Daddy" in their voice clips.
Valentine's Day Confusion
Females, usually bachelorettes, sometimes react to Frey as a boy on Valentine's Day and cease presenting them as a "friendship cookie."
Pink Dragon Takes Flight
Using elementally enhanced fists to slam a Pink Dragon using the B,B,B,A combo will cause it to heal the dragon while it's on the air, making it float on the air for a while
There are times when the protagonist walks up to a villager who he/she hasn't talked to yet to start up a conversation with them, but they both skip the usual friendly greeting and immediately go through their normal dialogue routine. This is caused by repeated amounts of soft-reseting.
Mistress Trupin's Refusal
After beating Arc 2, Mistress Trupin, for an unknown reason, will not change your name. She will skip straight to talking, not giving the option of changing any names. The cause of this could simply be if you had not talked to her until this point, although it is not for certain if this is the case.
Margaret's Demon Note
At times when Margaret pulls out her harp, she will continuously play one note. This is solved by simply walking out of the area and walking back in.
There is a glitch where, for no apparent reason, the diary will display the top word 'Save' on the diary above the characters, in Japanese. It can be corrected by leaving the diary, and re-entering.