If you place your cities aggressively in relation to a neighbor Civ, you have a good chance of at least a threat of Loyalty issues. Getting a governor, garrison and monument(?) up seems to help this. I find this to be an early-game problem as I like to settle near the neighbor I've selected or a first conquest. Once you take out the influencing nearby city this issue disappears from the one you built unless the one you captured is liberated or flips back. I have this situation arise a few times, but during my most recent game, I also received an Ancient Era historical event credit for daring to settle so closely to my neighbor. Not sure why I got the loyalty problems without the aggressive settlement credit in the previous games, but perhaps the distances are calculated differently. A related question is what Robert the Bruce considers to be a neighbor if you want to conquer other Civs without annoying him. Guessing it's a related number of hexes distant from any of your cities or any of their cities for each of these calculations, but the specific number be different for each one.Well... I rarely have loyalty issues even in my border cities, if I have loyalty problems it's during conquest and thus far I've been able to avoid an actual city flip (usually via blitzkrieg tactics, eliminate the enemy as quickly as possible and flipping isn't a big deal). So I don't feel like it's the wrong choice, but I suppose there might be cases where I'd want to put it elsewhere? Maybe.
Loyalty problems if distance < L hexes from city belonging to another Civ. Compounded problems for each of rival city within that range. (Might be offset by degree of proximity of your own cities?)
Aggressive placement event score if distance < A hexes from city belonging to another Civ. Must not have earned this placement earlier(?)
Neighbor rule violation for Robert the Bruce if distance of city you attack < N hexes from city belonging to you.