Being through the game recently, I am not surprised Goldenrod Underground was a challenge, it is very confusing and even though I solved it through trial and error, I still don't know what I did. Olivine Lighthouse is the real surprise, as it felt quite obvious to me.

This writeup on the underground puzzle is worth reading, it's a pretty baffling "puzzle" design. https://pokemow.com/Gen2/ShutterPuzzle/

That said, it's definitely Gem's fault that it struggled so long, considering it ignored the NPCs that give clues.