She could come off as a tyrant at times. "Tuvix," "Equinox," "Nothing Human," etc. I think the problem was two-fold:
1. She was off on her own, with no Starfleet to check her authority
2. She was written so inconsistently in terms of her principles(one week she's a Prime Directive fundamentalist, the next she's flexible) that it made her seem like she was on arbitrary power trips sometimes.