Just finished a complete playthrough of .400 after doing a playthrough of .362, and while I didn't encounter anything game-breaking or progress-halting, I did find some bugs:
.400 bugs:
Crystal Room Green Achievements section:
-Number of [enemies] purified does not seem to match the number of enemies defeated via Fertile Blessing skill. Do encounters with multiple enemies count double or triple?
-"NPC Pregnancy Growths" crystal will not advance in number after unlocking the achievement.
-"[Character] Seeds Birthed" crystals count the total number of birth sequences (as shown in the save screen), not the number of seeds as implied in the text. (This may be a regression; it was accurate in .362)
-Pregnancy "Gab" Messages will automatically revert to older, unvoiced lines after a character uses the Birth skill 20 times.
-Pregnancy "Gab" Messages stone text does not reflect what the current status of a character's gab messages is set to; it's thus rather confusing.
-After resetting "Gab" Messages to newer/voiced lines, the gab messages stone cannot further change the options.
Leah: Leah's new gab messages for Power >300 to 400 are unvoiced.
Quest Log: "Fertile Overgrowth" is the last main quest to update the quest log. The Bee Queen, Amazon/Lamia Island, Witch Academy, and Brasswall episodes do not update the quest log or Damia's Quest Advice when speaking with a Waystone.
Combat: If all enemies in an encounter are defeated with Leah's "Fertile Blessing", the combat will sometimes give no EXP/gold reward. This appears to be linked to the enemy type.
Hiyokuna the Kitsune: Hiyokuna the Kitsune appears to be missing from the .400 build. Nimune the fortune-teller still points to her location on the outskirts of Royal City, but she will not appear. (Presumably she was dummied out to the lost spirits now being used for rebuilding the mansion).
Silent Temple:
-Once the temple is restored, the green-haired angel-merchant's inventory does not accurately/fully reflect the variety of crystals unlocked.
Leah's Mansion (Restored):
-After being fed enough fertilizer, the Blueberry Plant-Girl will give you Oversized Blueberries. These items have no description and while they can be consumed, appear to have no function.
-After giving Celia all the artifacts, her demi-goddess sprite will sometimes get stuck and loop the same teleport animation, making things very bright and noisy, especially in the southeast quadrant of the mansion.
-Sapphire the Bunny Girl can be recruited and will have an initial cutscene in the upstairs wing of the mansion, but will then disappear from the area.
Royal City: The pompous innkeeper will never prompt to show proof of admission to the Witch Academy. (This appears to be a regression from version .362 where this interaction worked).
Brasswall: Most NPCs do not have idle conversation; some merchants are not enabled. The basement tunnels are not highlighted/marked as to which ladders/doors are functional.