The internal resistance warning is a warning, so the profiling continues regardless. The warning is that the internal resistance calculation ended up with a negative resistance. To understand this, the theory behind the internal resistance calculation needs to be understood.
Battery profiler discharges the battery with a high discharge pulse and a low discharge pulse. When the switch from high to low happens, the voltage (VH) and current (IH) is measured . Then when the switch back from low to high happens, the voltage (VL) and current (IL) is measured. The internal resistance is then calculated by Ohms law Rint = (VL-VH)/(IL-IH) The currents are negative. If the battery has a lower voltage in the end of the low discharge, than the voltage at the end of the high discharge, Rin will be negative.
To avoid this do the following: