http://whoismonsanto.com/10-things-monsanto-would-love-you-to-believe lots of references to studies here on all aspects of GMO.
Here's a study on GM crop yields: http://earthopensource.org/gmomythsandtruths/sample-page/5-gm-crops-impacts-farm-environment/210-2/
My main issue is that they don't really understand what they are doing. Its like trying to learn to code without a manual. They are at the copy/paste stage where they can isolate a section of code, which they can't read, but they know what it does, so they copy it from one organism and paste it into another organism. Unfortunately code in one area affects code in all other areas of the program.
Not only that, but DNA is read in two ways: the direct reading of alleles, and the reading of the proteins once folded. Its kind of like reading the first letter of each line of a page and getting a completely different message for something else. When you start copy/pasting stuff around you mess up the 2nd message. Combine this with protein and gene networks and you end up with massive issues, which they do not understand.