The single most common programming pitfall is trusting an empirically constructed software emulator to be a reliable program for verifying that your code performs correctly.

Other minor ones I can think of are not waiting for the PPU to stabilize on reset, writing to sprite memory manually, (don't ask me why people keep doing that) updating PPU memory, palette memory or sdprite memory outside of vblank and misc. IRQ issues such as not SEI:ing at reset or forgetting to initialize $4017. And of course, lots of homebrewn "NES software" still assumes that memory is set to zero at reset.