Hi,
By default the ble_app_template example use pin P0.06 for transmitting logs. You'll need to change this as the pin is connected to a LED on the nRF52840 Dongle. You can use any of the pins that are routed out on the PCB such as P0.26. You'll need to change NRF_LOG_BACKEND_UART_TX_PIN in the sdk_config file.
regards
Jared