When using auto throttle during manual flight, especially during approach and landing, there may be several pitfalls depending on the aircraft type and auto system.
For example if the aircraft enters the flare (A/T retard phase) slightly steeper or with a higher rate of descent then the reduction in thrust is perhaps not what is required. Without thrust intervention, only pitch control is available and if used excessively may result in a high nose attitude with risk of tailstrike or reducing speed more quickly than in a normal flare which incurs other risks.
Alternatively if the approach is shallow then the retard mode may operate early (lower Rad Alt), again requiring pitch control to regain the approach angle and control speed, which may be reducing rapidly. See the accident here:-
Transportation Safety Board of Canada - AVIATION REPORTS - 2007 - A07A0134
In addition some autothrottle installations are mildly destabilising in pitch; although not obvious to the crew this may increase the likelihood of arriving at the flare steeper or shallower than planned.