I would normally use Eclipse avr-gcc plugin and (avr-gcc compiler from zaks https://blog.zakkemble.net/avr-gcc-builds) to develop firmware for AVR MCU.
The MCU ATMEGA328PB has extra timers (3,4), SPI1, TWI1 etc. I am experiencing situation where after compiling the code, any of these extra peripherals’ interrupt vectors will be handled, it does trauncate. The avr-gcc compiler only handles the default 25 vectors of the ATMEGA328P.