A most likely finish for a CNC milled flat would be longitudinal marks, very smooth, if the cutter was sharp. If dull, the finish could have some longitudinal scuffing and tearing. A cutting tool typically would be an end mill, and used in a vertical mill. That's where the spindle is vertical in relation to the work table. The bit looks somewhat like a router bit, with spiral flutes on the sides of the tool. In a CNC you can mill very smoothly with the side of the tool.
If the flats are different, there can be many reasons. One might be that the part did not get clamped the same every time after indexing. Or that the fixture wasn't bolted down well, and it moved under cutting pressure. Many more reasons can be invented.