Check the Plot (of the City).
I bet that there is a Native Unit (of Logan) on that City Plot.
So for the game you are not just moving to your City.
You are moving on a Plot with a Unit of another Nation.
Thus it asks if you want ot attack.
It has to do that otherwise you could never attack Units in friendly Cities.
Summary:
If there is a Native on that City Plot everything is working 100% as designed.
Otherwise we have a bug which we need to analyze.
You are right - there is a native brave of Logan in the city.
Spoiler :
However how does that work? I mean only a few turns ago I did capture that city from the french and did not have that warning, so there would have been no native Brave there. How would he be able to enter the city AFTER I had conquered it from France but without being at war with Logan?
And how would I get a military unit in the city now for the case that it grows and would plunge into unrest? Do I have any way short of declaring war to evict him?