OK, In the scene where the Anaconda comes on the ship and breaks through the window and gets shot, the snake moves his head, and you can actually see the strings on the Anaconda.
I noticed this too but the strings don't bother me as much as how fake the Anaconda looks. With today's technology, I'm sure they could have used a small anaconda looking snake, took a shot of it hissing and such, then blew up the image. At least it wouldn't have looked as fake as the 'puppet' did.
One thing you have to think about is that the movie seemed to be cheaply made with poor special effects and all. Maybe they just couldn't afford to use better technology.