A couple recent studies have raised concern that certain corn rootworms are becoming resistant to the Bt produced by biotech corn. See for examples this paper in the Proceedings of the National Academies of Science by Iowa State University entomologists published last week (some of the same authors seem to have a similar paper published in 2011 in PLOS ONE) and this paper published in Nature Biotechnology this summer. The most recent study has prompted quite a bit of attention on the web from outlets as varied as Wired and Grist.
Any pesticide (biotech or not) has the potential to become ineffective over time due to the development of genetic resistance in insect (or weed) populations. Plant genetic companies, knowing this, tried to implement several strategies to slow the spread of resistance: such as developing several types of Bt that produced different insect-killing proteins (which appears to have had only limited effectiveness) and the planting of refuges. Refuges refer to the planting of non-Bt corn near Bt-corn, which reduce the selective pressure on rootworms and other pests, and thus potentially increases the length of the effectiveness of the Bt trait. Originally, corn farmers were supposed to plant a certain percentage of their acreage in non-Bt corn as a refuge, and more recently, we have seen refuge in a bag - the Bt seed is delivered to farmers premixed with non-Bt seed.
Some sources place the blame on the development of resistance on biotech companies lobbying for lower refuge requirements or on farmers for failing to observe the requirements. That may be partially true. Any individual farmer likely faces an incentive to free-ride off their neighbor's refuge (something that can be eliminated with the "refuge in a bag" concept), but it strikes me as incredibly short sighted that biotech companies would willfully advocate for policies that would reduce their long-run profitability (or it may be their interest to allow Bt resistance to develop if they have other products in the pipeline that become more valuable as Bt resistance develops).
As I see it, the real challenge here is Mother Nature herself. Agriculture is inherently a struggle against nature. We have become so accustomed to seeing crop yield gain, that sometimes it is easy to forget that one of the biggest challenges is simply trying to keep up with nature's adaptations to the latest varieties. The natural state of affairs is yield decline - not yield increase. Seen in this light, science and technology seldom offer a one-time fix. It is a constant struggle. We find a solution. Nature responds. We try to find another solution. Nature adapts again. And on and on it goes.
No doubt there are many who argue that we should step off this technology treadmill. We probably can find ways to better work with (or at least accept some drain in efficiency from) natural pests, and that may be one of our adaptions. But, I think it is foolish to think we can ever really step off the treadmill. There never was or will be some perfect ecosystem equilibrium. Bacteria, insects, weeds have been and always will be evolving to get the upper hand on their competitors (that's us and our food crops) and we will do the same. Our best bet is to try to stay one step ahead knowing our natural competitors won't be far behind.