Answer: I don't think rabbits nesting would leave long term damage to the soil. Based on your description it is possible there is some type of disease, possibly even a soil-borne disease, in those spots which is infecting your new plants. One approach is to replace the soil in those areas, another is to add good quality compost to it to try to introduce additional "soil life" that will outcompete the disease. Also be sure to clean up and remove all of the debris from the dead plants. Another possible cause might be that the soil is shallow in those spots and dries out quicker than the rest of the bed, or that the drainage differs and those spots are especially low and ewet or some other physical reason like that. You might want to see if your Penn State extension can diagnose the cause for the dieback and based on knowing that, decide what to do next.
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