An employee can file an EEO complaint about anything he wants. There is no prohibition on that. The EEO Office, when looking at the allegations in the complaint, should then dismiss any part of the complaint, or the entire complaint itself, if there is no covered basis (under Title VII, Rehab Act, etc.) alleged.
For example, if I am claiming a hostile work environment because I am a Dallas Cowboys fan and my supervisor is a Philadelphia Eagles fan, I can file a complaint. However, the EEO office should dismiss it for failing to state a claim upon which relief could be granted. Or, if I am alleging that a “personality conflict” is the issue there is no basis for a discrimination complaint because I have not claimed the conflict is based on gender or religion, for example, that should be dismissed as well.
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