How about that scene where you find Citan's family for the second time? Midori still behaves like she did when we first met her, but the Chu-Chu nearby insists on her being quite the chatterbox. Did she clam up when Fei entered the room? Or is it just implied that the text box shows the conversation only partially like the bulk of you talking with unportraited characters goes?
The possibility of it being exactly what it looks like - Chu-Chu talking aloud as if responding to someone we can't hear - is not exactly a very subtle one, but it (in my eyes at least) looked so much like one of those acceptable breaks from reality I as a player deliberately ignore in order to submerge myself in the video game medium that it didn't merit anything more than a small note in the back of my mind as the majority of my attention was occupied with more immediately relevant plot threads. Looking back on it, it feels like the narrative didn't even try to hide it - maybe that is why it waltzed right by me so effectively?
Same with the first Id reveal - there are details about it strewn all over the place and at least some of them pinged the 'something is not right with this picture' sense, but I didn't go 'A-ha!' until Citan dropped the bomb directly. IMHO, the way it is done adds some real replay value to the game.
Not so much with Grahf and Wiseman though. While there are some quite neat plot turns to them in the story, I don't remember there being enough details to connect the dots or at least make the player particularly suspicious before the reveals happen. If Xenogears was a manga, I would've said that these plot turns were conceived at a later date and then retroactively put in the plot and adjusted to not contradict anything when the author decided to scrap their previous plan for these characters - or just simply didn't have a firm idea of where they would lead the plotlines when they were introduced.
The scene at the end of Disc 1 where Citan presses Fei into letting Id out with a few choice words. Good doctor refers to Elly as 'the most important person in your life'. When I went through that scene for the first time, I thought it was the usual JRPG tripe of pushing male and female leads into a pairing regardless of how plausible it looked and throw around gems like 'look into your heart, you know it to be true' and so on and so forth. I don't know about you, but that was among the first thoughts I've had during the first meeting with Elly and I thought the game was starting to push that in already.
Now that I've completed the game... Oh, the main pairing still happened and I still feel it was shoehorned in just because 'this is JRPG, it is supposed to be like that'. But knowing what happens on Disc 2 and knowing Citan knew at least a part of that information, I now believe it was said with quite a different meaning in mind. And it wasn't 'love' - at least not 'pairing love'.