There are currently two major bugs I've discovered:
The first one is during Day 11 in Aris, after Kiligan and Mac entered Purescale Entryway and received Imperfect Lustre Amulets, an error screen occurred that cannot be fixed with Ignore. (By using Trailmarker in the title screen, the player can continue, but lost the Necklace and the Hammer which were given in Aris)
The second one is during Day 8 in Spiceport City, after Kiligan regrouped with Taavi and Mac, Izhashi called them into an alley. An error screen happened right after Mac said: "I didn't know what to expect meeting up with the pirates, so I thought it'd be good to bring it just in case, eheh..." and this error blocks the player from continuing the game completely