These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Brilliance: The problem with a Time Enforcement Agency is how do you Set Right What Once Went Wrong when your memories are changed? Simple. You make a Database in the Jurassic Era, so that no one can access it but your agency, and it would be destroyed long before any humans evolve.
The third game allows you to do a lot more with the people and scenery, including incredibly elaborate changes to Shangri-la, which would seem to violate the rules of the last two games. Until, of course, you realize all three will be destroyed in 24hrs and have no effect on history... (See Fridge Horror).
Fridge Horror: You meet a lot of nice, friendly, funny, and endearing characters while time-travelling in the third game. Every single one of them will be die horribly in twenty-four hours' time when the warring aliens destroy the three ancient civilisations. Yes, even that cute kid in El Dorado.
Fridge Logic: How did Michelle return to her own time after she abandons her suit in Atlantis?
Possibly through use of the suit's secondary features. In the 2nd game, in the intro, Future!Gage is found and apprehended by a fellow suited time travel agent. He at the time does not have one. The same beam he uses on Gage is equipped on Michelle's suit. She conceivable could have used this to boot herself to the time you find her in.
Or maybe kit bashed something to activate the recall function. Or maybe there was only enough power to return her or the suit.
Nightmare Fuel: Lots of it, particularly the underground section of Mars (scary ambient music, big scary robot that kills you in a scary way, the Shield Generator, with more scary background noise, that skeletonizes you if you take too long solving the puzzle, and the Maze with the music that slows down as your oxygen decreases, and finally fades to heavy breathing and heartbeats), and Sinclair's lab, where you get shot with a dart and are slowly dying, while creepy/sad music is playing.