The length of the pendulum varies with temperature, so that means you get an error that varies with temperature. This can be compensated for, but not easily.
The rate varies with the value of g, nominally 9.8 m/s², but that value varies by a few tents of a percent as you move around on the Earth or change altitude.
Pendulum clock cannot be use by something in motion, such as a ship.
Large and bulky.
Needs a mechanism to keep it moving.
and, yes, from other answer, rate is very dependent on amplitude of swing.