So I go to the first garden, get frustrated with the seemingly pointless donor glyph drawing thing, visit the other chambers, collect a heart, go back to the first garden, kill some bats, go to the second chamber, kill two bats then I go to that yellow node, a cutscene plays with some dude saying some vague stuff and the game resets.

What is going on? Am I dying and this is how the game is telling me it is game over? Or is it some bug?

Does a brief cut-scene trigger just before the rest? If it does, then yeah you died which makes you go back to the title screen and load an old save.