I only played The Moment of Silence german demo, but I didn't notice any obvious glitches. The 3D character(s) incorporation looked ok to me, at least in those few scenes I've seen in the demo.
From technical point of view, IMHO it will be always tricky to integrate 3D characters into 2D scenes, because you always have to fake something; namely the 3D character obstruction by 2D scene elements. Also the rendering method for the characters is (naturally) different from rendering method of the scene, same goes for the level of detail (low-poly characters vs. high-poly scenes). There are things that may help to hide the differences, such using the right lighting, antialiasing etc., but it will always need careful planning when designing the scenes.
Just my $0.02...
We were talking about it at IRC with Jerrot, who happens to own the final version of TMOS, and according to him a bigger problem is, that the game changes the camera angle way too often, confusing the player. I think we all know this situation from games like Alone in the Dark or Silent Hill. Another thing to be careful about when designing the scenes.