The mod's author himself admits some of the puzzles are a bit tough and has been revising them slightly in updates, and even goes so far as to link YouTube solutions, by chapter, in the tutorials section of the mod's page.
I was baffled for a while at one point in Chapter 2, when it appeared I had followed the alchemical steps properly, only to later discover another series of laboratory instruments in different room that also needed to be utilized. The puzzles are of varying difficulty, and can occasionally be quite challenging.