The APP doesn't show the cheapest combination of flights whatsoever. It shows what LH wants you to buy. For example: BCN-FRA-BER. Although flights with longer layover are much cheaper, those are not shown on the APP nor the web. The old engine of multiple segments (where you could select one by one) is now gone. I tried to book multicity vie LH web and played a bit with flights LH showed me. In this case I could get a better deal.
Example: BCN FRA 1245 and FRA BER 1600 (1h layover) was 180€.
BCN FRA 0800 and FRA BER 1600 (5.50h layover) was 120€ (not shown)
BCN FRA 0650 and FRA BER 1700 (8h layover) was 90€ (not shown)