GPIO Configured as Input OR Output
There is no good reason to wire a capacitor directly across an output. If, for example, the capacitor is discharged then it behaves as a momentary short-circuit when the output is turned on. This presents a momentary overload to the output. Similarly when charged, pulling it low will effectively present a momentary connection to V+.

On the other hand, as an input R and C behave as a low-pass filter. This could be used to debounce a digital input or stabilise an analog reading. In both cases it introduces a small delay in the response time.