To give one, the Gold Tabulas in The Ark of Napishtim (and, by extension, the Winged God Emblem) is definitely one of these. Various third-party titles like Taito's port of IV also have loads of these.
Getting the Black Tabulas is worse; you have to use a certain item that allows you to see invisible platforms, with no hint that it does so, and you don't obtain it until after completing the dungeon that contains said tabulas.
Goban tells you that the Mask of Eyes allows you to see hidden passages. In the TurboGrafx-CD version, there are the hints of "I saw that blue statue's eyes glow" and the outline of a doorway, but in other versions, there's nothing remotely hinting at the hidden doorway in the shrine basement. The Steam, PSP, iOS, and Android versions will draw slight defects in the lighting of the illusionary walls in the mountain shrine, but those defects are so subtle that they could be easily overlooked and could probably be completely lost if the display in use is of poor quality like a monitor that uses a 6 bit per color channel panel. The illusory wall in Darm Tower is has no visual defects, but Dogi will give Adol a clue to look for Raba in the hallway next to where he is hiding when he breaks Adol out of the dungeon cell.
The smartphone versions of Ys I shows you a couple of pictures that vaguely suggest that you must run into enemies' sides or back to land clean hits. There is nothing to let you know that you can also get clean hits by running into the sides of their fronts. The smartphone version of Ys II is even worse by not providing any tutorial whatsoever on how to physically attack enemies, so someone who did not buy Ys I would be clueless on how to attack enemies.
There are two puzzles in Ys I that are not solvable unless you Talk to Everyone, consult a walkthrough, or remember the solution from another game with the same puzzle.
One puzzle is how to get the silver sword. You need to find a roda seed and the silver harmonica in Rastin Mine. You would not know that you should eat the roda seed unless you talk to someone who states that it is a rare delicacy that everyone should try if they find one. Eating one grants you the ability to communicate with the roda trees. You also have to return the silver harmonica to Reah. She then plays a song that wakes the roda trees up. Otherwise, the trees will just mumble nonsense in their sleep if you approach them after eating the roda seed. Finally, you have to talk to the roda trees to get the silver sword.
Another puzzle is how to pass the Devil's Corridor. You would not know how to solve this puzzle unless you talked to Raba twice when he is trapped in the cell adjacent to the Devil's Corridor, remember the solution from Hugo Fact's route in Ys: Origin, or consulted a walkthrough.
The fetch quests where Adol has to find lost pikkards have no clues on where they are located.
Hey Baby, What's Your Width?, I Can't See You, But I Can Feel You, and Police Are On Their Way: During both games' Escort Mission, there is a single narrow passage which you must push your escorted character into. This will trigger some dialogue and give you the achievement (I Can't See You also requires you to be wearing the Mask Of Eyes while doing so).
No Reservations: In Ys II, there are four NPCs who will give you food if you give them enough gifts. Some are somewhat hinted at because they raise meat animals, but one of them is a blacksmith and is never hinted to give you anything.
Bill the Duck: You must give gifts to an NPC (once again, there are absolutely no hints as to which NPC this is) until he tells you that sometimes the ducks eat gold coins. Now you can examine the ducks outside and one of them will give you gold and the achievement.
Where's Aldow: You must use the Alter spell and return to the first dungeon, in the area where you found the Evil Bell. One monster will give you the achievement if you talk to him.
