This is definitely new since I played on Wednesday evening. Character sheet is using the current alpha, 3.0.0-alpha.63. Subclass is homebrew (initially to get that Disciple of Life bonus working correctly, which I note the new sheet still doesn't do), but the homebrew subclass (and spells) were working correctly when I leveled up on Wednesday (I know, because there was a problem with how I'd coded the 4th level bonus spells, so I'd just reviewed this.

Character (linked to my version, in case mods need to review).

The subclass still has the Life Domain spells, but I swapped out the official healing spells for homebrew ones that account for Disciple of Life. Those are the only spells in the 'additional specific spells' section of the Basic Information. However, I also added in a handful of spells, which I did by homebrewing the spells and changing the classes it was available for, so that they weren't showing up as always prepared. Again, this was all working fine on Wednesday.

But today, the following homebrew spells are showing up as 'always prepared,' when they're not in the 'additional specific spells' list, not granted by class features (the bonus spells are a text-only class feature in the homebrew builder), and the homebrew spells are available for 'Cleric,' not any subclass: Healing Word, Healing Spirit, Plant Growth (this spell is showing up twice - it's definitely homebrew, but I only made one copy). Some of the other homebrew spells I made for this class are not showing up twice, eg Prayer of Healing.

I have noticed that too, even sometimes when there is no homebrewer afoot.

Could you provide a link to the homebrew versions of those spells? I would be happy to take a closer look at what's going on here for you!

I don't think it's the spells, as I made them months ago (some over a year ago) and they were working fine until late this week. Since the only tweak to these spells is to make it available for the class, or to adjust the healing, the only change has been to 'available for' or the text on how the healing works.

• Healing Spirit - should not be autoprepared
• Healing Word - should not be autoprepared
• Plant Growth - should not be autoprepared, should definitely not show up twice.

But it's obviously not all of my homebrew spells being wonky, because spells like Cause Fear (Class Features UA homebrew) and Prayer of Healing (homebrewed for correct healing amount) are working correctly.

You can see on the character sheet (above) that I've put in notes on healing spells as well ("Kel heals 2+spell level") for tracking Blessed Healer. The autoprepared versions are all missing this note. I also had 11/11 spells prepared when I came out of my last long rest when I played on Wednesday and you can see I'm now down to 10/11 because Healing Word has gone from being manually prepared to always prepared.

Hello again! After some investigation it looks like this is a bug. The team believes they know the cause, and they're going to work on a fix. I'll update you when there's news. Thanks for the report!

Thank you!

I don't suppose there's an update?

Hi, this is now partially fixed but differently broken!

Working correctly now:

• The spells that were being autoprepared but shouldn't have been are now working as intended.

New errors not present originally:

• The homebrew version of Cure Wounds that gives me my Disciple of Life bonus is no longer autoprepared and the basic version of Cure Wounds, which I had customized to be called 'No,' so I didn't select it by accident has had its customizations removed. You can see that the customizations for Healing Word, which are the same, are still correctly present.
• Rinse and repeat but for all my domain spells that are affected by Disciple of Life: Revivify, Mass Cure Wounds, Raise Dead.
  • Looking at the subdomain, they've been removed from the Additional Specific Spells list. Not by me. I'm pretty sure they were there when I used this character a week ago, because I had to manually review everything before I could prepare my spells for the day, since I couldn't trust the spell list. I still can't trust the spell list.
• In my second level spells, if you look at the spells whose names have been changed to 'No,' there are two each of Continual Flame and Warding Bond. The first of each lists the source as the PHB, and the second of each have instead the Version: line, indicating that they're homebrew. However, I don't have homebrew versions of these spells in my collection (technically, I have versions I made then deleted, but they are named differently than what appears here). The character sheet is not in a campaign and never has been, so it's not someone else's homebrew.

This is not an improvement, especially the part where someone is editing my stuff.

I was hoping that the changelog fix related to homebrew spells might have fixed the issues I've now got with duplicated spells, but it does not. I'm also still waiting for an explanation regarding someone modifying my homebrew. I still don't know who, or why, or if restoring the spells they removed from the subclass homebrew will cause greater issues.

OK, and today I've found that my homebrew feat (just a reskinned luck) is also now missing from my sheet. I'm not sure when it was removed, but I didn't remove it from this character. 

Did the fix for this go out?  I *think* I am experiencing the same problem.  I created a Homebrew subclass, added some additional spells, then later removed the additional spells yet characters who take the subclass are receiving the now-removed additional spells.

This finally was fixed for me by the following steps (no idea which one was the actual fix):

1. Remove subclass from my collection.
2. Remove subclass from character (edit character, subclass, switch back to --)
3. Add subclass back to my collection.
4. Wait for subclass to show up as an option for my character (can take up to 30 minutes and requires a refresh it seems).

Once I did that, my subclass was no longer giving out spells I had removed from it.

What you're describing sound like the general server lag issue that's been going on for a bit. My issue was 'I changed nothing about any of my homebrew, but suddenly some spells are showing up multiple times,' with a later, unresolved round of 'staff removed feats and spells from my subclass without notification or explanation.' My issue didn't involve 'spells I removed are still there.'