1. Failing to interview both the accused and his witnesses as well the accuser and his witness.
Interviewing only one side or neglecting to interview potentially critical witnesses for one of the sides will make the investigation look particularly unfair and biased. It is the employer's duty to interview and gather information from all the available sources on both sides, before making any conclusion or taking action against an employee.
2. Delaying the investigation
While there is no bright line rule on how long it should take for the employer to start and complete the investigation, the sooner you start the better. This is especially true in cases where the employer is a large and well-funded company with resources specifically allocated for ensuring workplace safety. Waiting for weeks to initiate investigation may be unacceptable, especially if the alleged conduct is egrigious enough, such as sexual harassment, or violence / threats of violence at workplace.
3. Having the investigation conducted by a manager who is biased
To be fair, the investigation has to be conducted in an unbiased manner. If the investigation is run by the manager who dislikes or favors the accused or the victim for personal reasons, that investigation is likely to be skewed and lead to unfair conclusions. An employer should consider having an investigation conducted by an impartial investigator or an attorney in order to make sure that the results of the investigation are actually useful.
Employees can use one of the above issues in workplace investigations in proving their discrimination or retaliation. For instance, consider a situation where an employee applies for FMLA or disability leave. Shortly after making that request, a complaint of harassment is submitted against him, and he is terminated without any investigation or after a very shallow and incomplete investigation takes place. The employee can later argue that along with timing of his termination relative to the medical leave request, the fact that the employer didn't bother to verify the accusations before terminating him further evidences that the real reason for termination is medical leave discrimination and not the harassment complaint.