It was predicted, in a way. See Brooklyn Community Board 2's 9/29/06 comments on the Atlantic Yards Draft Environmental Impact Statement and General Project Plan:
Community District 2 is experiencing a significant increase in the number of disease-bearing rats, which can be attributed to the large amount of construction currently underway. Community residents have reported that the rats are regularly seen scurrying in and around their homes. In light of the prospect of the massive demolition, excavation and construction associated with this project, it is anticipated that the underground habitats of Brooklyn’s rodent population will be disturbed. Containment plans to mitigate the inevitable disturbance and escape of large numbers of rodents into neighboring communities needs to be specifically defined and coordinated with appropriate governmental agencies in advance.
Presumably the construction of one tower, B2, next to the arena, will have far less of an impact.