As of version 3.03

Major

• Refreshing during battles will destroy health bars and create several issues with the JavaScript. This is due to the nature of Twine and cannot be fixed. Just try not to refresh during battles. Fixed in 1.26.1, amazingly. Refreshing in general is still not recommended.
• The Inventory class does not revive correctly on a save load. Fixed in 0.99
• <<deathcheck>> causes an error when trying to remove some effects. I suspect the issue is Protector; will investigate. Appears to be fixed as of 1.25
• Equipment will produce strange effects if the onEquip and onRemove functions are changed between save game versions. Fixed in 1.08
• Top-of-round code will run additional times if an enemy uses an instant action as their first action. Fixed in 1.26

Cosmetic

• When an applied effect has its duration extended, a blank line is generated. Fixed in 1.10.3
• A line break isn't generated for the death message when an enemy is defeated by DoT. Not sure if this was ever fixed, but now irrelevant with the DoT UI revamp
• Effects with blank removal messages still force the player to click through the end-of-round passage. Fixed in 1.08.5
• Party sizes greater than 3 create weird effects with the command display. Fixed in 1.09
• The unequip button only travels to the edge of the equipment description box, not the larger actor box as it should. This is due to some HTML finnickyness I dread interfering with. Fixed in 1.07
• Actions with long descriptions will run off the page when actions are compressed, making them unreadable. A better popup method is needed. Fixed in 1.25
• Shake animations sometimes don't trigger when the action affects both an enemy and a puppet.
• Characters appear dead before the killing blow is struck during animations. Fixed in 2.03
• Action/item use notifications visibly switch back to the default styling before fadeout.
• The battle grid "flickers" as it's being updated when moving characters around.

Minor

• The enemy action loop doesn't quite work as intended; if there's an else clause (as there should be), the probabilities are thrown off because a failed action will automatically be changed to the default. Is this really a problem though...? Maybe it's best if it does work that way.