I've noticed this as well. As far as I can tell, the issue isn't the game putting the map marker in the wrong place - the map marker object itself (comprising the marker and its text) is incorrectly centred. It's centred on the point between the marker and its text, when it should be centred on the centre of the icon. If you place a marker and then zoom in and out on the map, you can see the marker scaling on this central point. This makes precise marker placement impossible, as its precision is dependant on the current zoom level.

I've noticed this same issue since the 1.3 update. It wasn't happening beforehand, and it doesn't happen with freelook. When using freelook (even with TrackIR running), freelook rotation seems scaled correctly regardless of zoom level. When trying to freelook with TrackIR, rotation is scaled correctly while at normal zoom, but seems to be at about 0.5x scale when zoomed in (in other words, you can use TrackIR to turn your character's head 90 degrees to the right, then when you hold down the zoom button, the view will zoom in and your character's head will only be turned 45 degrees to the right - returning to 90 degrees when releasing the zoom in button).