1- Muscle Attachment Points
This is the first and foremost requirement of powered flight: you need something to move the widened area. Kuehneosaurs (along with several other groups of mesozoic reptiles) did not have any muscle attachment points for their elongated skin.
On the top is a koehneusaur and on the bottom is a pterosaur. As you can see from the image, the major difference in their forms is that the koehneusar's skin membrane is not attached to either the arm or the thigh region and there no means for it to flap its membrane up and down on its own will. On the other hand, the pterosaur's membrane is attached all the way from its shoulder to the elongated 4th finger, providing it with a very viable power source (arm muscles).
The most important flaw of the koehneosaurs (as we understand them now) was they were unable to flap their skin membranes.
2- Surface Area Of Flight Membrane
As you can see in the image above, there is a major difference in the membrane size versus aggregate body size ration between the koehneosaur and the pterosaur. Birds and bats also have larger wing size to body size ration than koehneosaurs.
Notice that when we say body size here, we are referring to body weight. So another problem with koehneosaurs was that their membranes (even if attached to a muscle) were too short to allow them long distance flight.
3- Rib Obstruction
Since koehneosaurs' skin flaps were not attached to any limb, they had a series of elongated ribs to support their membranes from hanging loosely. In case they had their membranes attached to any limb, these ribs would prove to be a major obstruction in flapping the membrane. Their ribs were made for support, not movement, and the attachment joints of these extra ribs to the ribcage were designed for rigidity, not flexibility. If a koehneosaur had its membrane attached to a limb and then quickly flapped that limbs, there is a major chance they would have mortally injured themselves by breaking some of those supporting ribs.
So the third point of anatomy obstructing them from powered flight was that their rib joints were inflexible (to support the membrane) and did not allow for the movement of the membrane over wide angles.
4- Limb-Joint Structure
Vertebrate creatures with powered flight (pterosaurs, birds, bats) have specially designed shoulder joints which makes it easier for them to move their wings/arms up and down. This is an exception, not the rule. All non-flying vertebrates have shoulder joins which allow arm movement in all angles, but encourage arm movement in forward and back angles.
In case koehneosaurs' membranes were attached to their arms, their arm joints would have to undergo some visible changes to facilitate up and down motion of the limb, which would help provide the required thrust for flight.