It suggests a strong dislike, not just a mild annoyance or typical disagreement. She has had it in for me ever since I got the promotion she wanted.
Pro Tip 2/3
Subtle Intention
The phrase implies a covert plan or intent to harm, not necessarily through direct confrontations. After the prank I played on him, I'm sure he has it in for me now.
Pro Tip 3/3
Long-term Hostility
It can imply a long-standing resentment that might not easily be resolved. Mia has had it in for her co-worker for years, blaming her for a missed promotion.