Proper acceleration is the absolute one, it is what is measured by accelerometers. Coordinate acceleration is relative to the coordinate system.
For example, consider an accelerometer on the edge of a rotating disk in deep space. The accelerometer measures the centripetal acceleration. Considered from an inertial frame this accelerometer reading matches the second time derivative of its coordinates, so the coordinate acceleration and the proper acceleration are equal. However, now consider the disk's rotating reference frame. In this frame the second time derivative of its coordinates is zero, so the coordinate acceleration does not match the measured proper acceleration. To explain this we include a fictitious force, the centrifugal force, which counteracts the centripetal force. Such fictitious forces, being fictitious, are not measurable by accelerometers. Both frames agree on the proper acceleration (the measured acceleration in each case), but they disagree about the coordinate acceleration (equal to the measured acceleration for the inertial frame, equal to 0 for the rotating frame).