It's been awhile since I've read in depth on this subject, but I believe when the authors say in the abstract "Nevertheless, in specific districts and years, Bt cotton may have indirectly contributed to farmer indebtedness, leading to suicides, but its failure was mainly the result of the context or environment in which it was planted.", they're referring to analysis showing that the suicides mainly correlated with regions where the banking infrastructure was under-developed (and good loans were not available to the farmers, to help them through rough times) that were subsequently hit with a bad year; within those regions, farmers who had planted Bt cotton were slightly worse off than farmers who hadn't, but it was a weaker correlation than the rest.
(But again, it's been years since I read in depth on this, and I could be confusing this paper with another.)