Artist Disillusionment: What resulted in Ueda's departure and other staff members, due to feeling a "sense of crisis" as a result of the delays. Many moved on to other companies, while Ueda the rest founded genDESIGN. Fortunately, the studio decided to help finish the game via contract with Sony.
Blooper: When the companions have made it to the top of the tower, the boy runs to the edge and says something that doesn't get translated. One might assume it was an oversight.
Creator Backlash: Even though its clear from gameplay footage the giant baby griffin and boy care about each other very much, Team ICO are not happy to comment upon the relationship between Trico and the boy. Stating its up to the viewer, the audience, to interpret whatever they wish beyond their hostile-first-meeting.
In part, these delays are a function of Ueda’s uncompromising vision and unusual directorial process. When he is working on a new game, he begins by creating a mockup short film, which gives his team an impression of the feelings he wants to elicit but doesn’t get into technical details...Sony, for its part, indulges Ueda’s perfectionism. When asked, in 2015, whether the company would like to work with him on another project, Shuhei Yoshida, the president of Sony’s Worldwide Studios, said, “Everyone would."
Dueling Games: With Microsoft's Scalebound. Both are games involving human protagonists accompanied by giant monsters set in a fictional world. Both are to be released in 2016 exclusive to the opposing console.
Subverted, as Scalebound ended up getting pushed back to 2017, then was unceremoniously cancelled early that year.
Jossed: Early in the game's development, Word of God said that the ending would be sad. This led to people speculating that either the boy, Trico, or both would die. The final game disproved all three, instead being a Bittersweet Ending.
Progress was incredibly slow, featuring several false starts, with Fumito Ueda announcing that he was leaving Sony, along with other Team Ico staff (though committed to finishing it via after contract founding genDESIGN), and rumors of cancellation due to a lack of information. For context on just how long it spent in development hell, keep in mind that the game started development for the PlayStation 2.
Ueda originally wanted the game to have a similar opening to Ico, with the boy waking up in a cage, but ended up changing it. He still wanted a part with the boy having to fight his way out of a cage, however, and added such a segment towards the middle of the game instead.
There would originally have been a button to press to make the boy grab onto Trico just like with Wander and the colossi, and Ueda didn't decide to make the grip automatic until the end, when he figured he wanted to make the feature of climbing Trico to be "easy for everyone".
One rumour has it that Ueda originally meant for the game to feature a real-life animal, but ended up creating an imaginary one so they could give it the behaviour and personality they wanted, instead of using a real animal, for example, a dog, and risk having people point out that it "would not behave like that" or "couldn't do that".
Ueda contemplated on the post-credit scene ending with showing two or more Tricos playing with their offspring, but went for the more subtle ending shot we got instead.
Word of God reveals some interesting facts about the game in its art book:
Despite what the game implies, Tricos do not only kidnap children, but may kidnap adults as well.
It has probably happened more than once that a Trico got struck by lightning and regurgitated its victim back up, but until you played as one of the victims it would never lead anywhere.
The dark Trico the companions occasionally encounter throughout the game is the opposite gender of the main Trico.
Ueda got the idea for the game when he saw the reactions people had to Agro's "death" and later return in Shadow of the Colossus. Seeing people react so strongly to an animal companion inspired him to make a game centering around the protagonist's relationship to an animal.