As stated in previous posts, the tapered nose and tail shape is more aerodynamically efficient compared to a "Straight sided cylinder and Nose Cone" design. At the time of the design of the first A4/V2 reduced scale prototype (the A3 around 1936) the best understood shape that was known to be efficient at supersonic speeds was the high velocity bullet or shell, with the characteristic ogive nose and truncated ogile tail. There was a huge amount of ballistic testing data available for this shape, at a time when supersonic wind tunnel data was very scarce. Complex curves are harder to manufacture however, so it was a trade off of reduced risk and higher aerodynamic performance against manufacturing cost. Is this an example of over or under engineering ? Not sure. To me its an example of good engineering in that it reduced development time and risk while not introducing unacceptible levels of manufacturing complexity.
The choice of stringer and rib construction, with separate internal tanks was another technically conservative decision. Experience in aircraft construction meant it was fairly well understood. Not so much for monocoque construction. Wasserfall was a mix of monocoque and rib and stringer construction. But it was a smaller, later missile with pressurised fuel delivery (rather than turbo pumps) so required stronger more rigid tanks, more suitable for acting as a monocoque. The monocoque section required new welding techniques to be developed, caused some problems with wing attachment, impossible to fix tank leaks, and made for a more delicate missile. A4's were launched with holes punched in them through mishandling during transit. Because the outer skin wasnt the tank skin, they were still flyable.
With hindsight going for stringer-and-rib for A4 and partial monoque for Wasserfall look like very reasonable design choices. None of these choices seem to be "problems" (the title of the post) but fairly sensible compromises given the state of the art at the time and the need to get systems operational when they could be of some use. As one wag quipped "the war won't wait for Prof. von Braun".
The greater availabity of wind tunnel data and the operation experience gained with the A4/V2 made it clear that the less optimised cylindrical body shape was an acceptible aerodynamic compromise, while being a lot easier to manufacture. So when von Braun and his team designed the Redstone for a new customer, it had a much simpler profile. This continued right up until they put a man on the moon with the Saturn 5.