Not necessarily. I see three possible explanations:

1. OP's friend was within regulations, and the person who inspected the checked baggage screwed up. As referenced in post #5, there are regulations governing LI battery transport on passenger aircraft, but these regulations could have been misinterpreted by the baggage inspector.

2. OP's friend's batteries would have met the regulations if packed with their tools, but OP's friend filled one case with tools only and one case with batteries. As a result, the batteries were not "PACKED WITH OR INSTALLED IN EQUIPMENT" as required to exempt them from prohibition as cargo on a passenger aircraft.

3. OP's friend's packed batteries with primary cells containing over 5 g of lithium and/or a total of more than 25 g of lithium (e.g., 4 g of lithium per cell, 7 cells).