Eh, never heard of that. Not saying you haven't read or been told that, but I'm guessing this is the purely annecdotal recounting of a freak problem.
The best products from any company can die freakishly. The question is whether there's a real trend towards that -- and I don't think there is.
Both of these companies have reputations for producing reliable, sturdy frames. Myself and a lot of my riding budies have spent lots of time on Giant road frames, and I've never encountered or heard of a problem with cracks. With the exception of some versions of the Fuel MTB frame, the same goes for Trek.
With their traditional frame sizes, Trek is arguably easier to match to a given rider; if you find a Giant that suits you, though, by all means, go for it. For the undecided, it's all about feel and fit.