I work in a lab where some of the graduate students study bees. They've mentioned that even "safe" pesticides have the effect of debilitating the immune system of honey bees and making entire colonies more susceptible to other types of chemicals as well as parasites and diseases. In addition, the combined effect of multiple types of pesticides labeled "safe" makes them unsafe.
The lab's bee hives are being used to study the effect of the phorid fly Apocephalus borealis, but they frequently encounter molds, varroa mites, waxmoths attacking the hives. There's also always unknown pathogens that cause the hives to start failing, but no one has really understood exactly what's causing the hives to start faltering.