1. Turning a single comment into an lengthy exposition and/or making every conversation a meandering, "thoughtful" tour through the writer's mind is generally a sign of pretentiousness. (See: Braid)
2. If you ever hear something along the lines of, "This isn't that type of story. It really doesn't have a single message but is supposed to be your own interpretation of the story," then it will probably be oozing with pretentiousness (See: Jonathan Blow and Braid). This also goes for games that couldn't be trying harder to deliver this idea, even if the developer doesn't actually say it (See: BioShock Infinite).
3. If there is a jarring disparity between the "artsy" sections and the "action" sections, then the game was trying too hard to be artsy and, therefore, can be labelled as pretentious (See: BioShock Infinite).
4. If the game feels the need to take a great story, such as The Sands of Time Trilogy from Prince of Persia, and "improve" on this by challenging your notions or making it more "intellectually stimulating", then the game is probably pretentious (See: Braid, BioShock Infinite).
5. If the end of the game is a meandering monologue with self-aware "insight" that is meant to explain the writer's vision, then the game is pretentious (See: Braid, BioShock Infinite).
6. If the game tries to tell you that its choices have weight, then be on the look out for pretentiousness. Sometimes the choices genuinely do, such as with The Walking Dead. However, there are games that go out of their way to make sure choices are not "based on right and wrong" but end up inevitably delving into taking the consequentialist side of the consequentialist/non-consequentialist debate (i.e. trying to be philosophically enlightened and non-dogmatic, but taking a strong stance on the side anyway). My time with The Witcher tended to show this side of the issue. On the other hand, you have games like BioShock Infinite, where the idea is to make choices mean absolutely nothing (the bird/cage or draw gun/yell at guy choices) or pull the most generic "tough" choice they can (is killing ever right?).
7. If you hear the phrase "I want to ask questions, not answer them," then be on the look out for pretentiousness. Some developers know how to do this. Other games, such as BioShock Infinite, betray that the writer had no idea what that comment meant, just that they liked it and thought it was a good way to look "enlightened" and "thought provoking".
8. If the developer makes a point to avoid "ludonarrative dissonance", then it is possible the game will reek of pretentiousness (See: Many indie titles).
There are probably more I can think of, but those eight tend to cover everything. Note, however, that I don't think pretentiousness is automatically bad. It gave Braid a little more character to be overly pretentious, and it fit the game whose main idea was thinking through puzzles. However, it can be a downfall of a game, because it creates a character that is completely at odds with itself, is rather pseudo-intellectual, and/or is just a bore to follow. BioShock Infinite falls in the latter category.