If the self-test finds errors, it will tell you whether both the MICTOR38 connector and the 10-pin connector or only the MICTOR38 connector contains failing signals. Double-check your connections and retry the test if this happens. The connections may be loose, or in the case of the JTAG connector; it may be connected incorrectly onto the pin-header. If the error message persist, it is likely that there is a hardware problem somewhere. New probes and cables can be ordered separately from the Atmel Store (store.atmel.com).
The most likely source of hardware errors are after connecting any of the signals in the Mictor38 or 10-pin connector on the probe to voltages exceeding the maximum limits of the Atmel AVR ONE! probe hardware. The maximum ratings for the probe hardware are given in Atmel AVR ONE! Features.