Plot hole: When the Illuminati are breaking into the tomb of the dancing light, Lara is watching them through binoculars. She sees them, and even comments about Alex. How did she see them through all the trees? There were loads underneath her.
Plot hole: If the ancient civilization wanted to stop people from ever using the power of the triangle again, why didn't they just destroy the triangle right then and there instead of splitting it in two and hiding the pieces? It would make sure that no one would ever get the power of the triangle and is easier than going to ends of the earth and creating all sorts of traps and challenges.
Plot hole: About Lara's getting inside the Cambodian temple, how exactly does plucking off a flower activate a mechanism that opens a secret entrance to it? (Over the centuries, none of those flowers ever withered or was plucked off by the wind, of course).