It's part of the game, as Dude0123 said, many scenes lack art still, as the game was originally text-only.
The main page here has mega links. You just need to download 0.35.1, and then the "update only" link, and apply patch 0.35.9 to 0.35.1.
Yes, download and apply the "old save compatibility patch" to your game. You will also want to enable the old save compatibility option in the debug menu for the sake of the fifth dungeon. The patch removes some of the functionality of a plugin—which causes this bug on old saves—so the debug option just does things manually to compensate.
That should be fixed by patch 0.35.2 or later. If you have that applied or find applying it doesn't work please let me know.
After you pick the first bunch, there's no notification when you gather them, as I thought that would be annoying to have text pop up on every batch. So is it possible you are pressing Z on the batch twice and getting that notification? I should maybe add a sound effect when gathering to avoid that. Could you check your key items and see how many elmsbloom you have? I tried to replicate this bug but everything seems to be working for me. Thanks.