... of an agency going bad?

- distracted during phone calls
- appointments mixed up
- not passing along personal requests to the girl
- different person answers the phone
- girls complain about unprofessional behaviour

What are the warning signs that an agency is running into problems?

That is good about passing on personal requests to the ladies. If you know of one please let me know lol!!!  

The ladies complaining about the agencies unproffesional behavior would seem to be a red flag to me. The other stuff I'd be less concerned about.