A big difference is also that things are sequential at the gate level. Everything happens at the same time. It’s almost like a massive multithreaded program. Also, propagation delays can make you pull your hair out if you aren’t aware of them when debugging. There’s also a possibility of unclean signals (not Vcc or GND, transition bouncing, etc.).
One level of abstraction further down, Gates are analog, not digital. If you don't clock things right, you could end up with huge currents going through two transistors trying to drive something opposite ways, and then lose the chip, or battery life, or an intermittent glitch.
