In 7 Wonders Duel, the instructions say when you are preparing the Age 3 deck you should remove 3 cards from the deck and add 3 random guild cards. I assume the guild cards should be shuffled in so I usually just put the 3 cards in random positions and shuffle the deck. However, the guild cards have different colored backs (they are purple like the Age 3 cards but are darker) so I can clearly see where the guild cards are and know where they are going to be when I build the oval-shaped layout. This seems wrong to me. Should I close my eyes when I shuffle the deck or is there a reason why they stand out? Should they go in a certain position when the cards are placed?
You are not doing anything wrong.
Looking at rules here it says :-
Return to the box, without looking at them, 3 cards from each Age deck. Then randomly draw 3 Guild cards and add them to the Age III deck without looking at them. Return the remaining Guilds to the box.
My other reference for this is playing the 7 Wonders Duel app. I can confirm that also places the guilds in random positions and the face down ones have a visible darker back.
As for the reasons you would have to ask the designer for the certain answer. However as a player its very useful to know if a face down card is a guild. Lets say your opponent is close to achieving military or scientific supremacy? if you are going to be forced to reveal a card on your turn wouldn't be better to reveal a card that you know cant give them an automatic win?
Like wise if you as a player are close to winning with military or scientific supremacy, would it be better to build a wonder granting those all important extra turns in the hope you reveal the exact card you need and knowing its not a guild increases that chance.