To be specific, the placement of the engine does NOT cause inherent problems, assuming the design is properly thought out. There are design considerations, to be sure, but not necessarily problems that can't be overcome.
In the case of the P-39, the design was not quite well thought-out. Yes, it had a driveshaft running under the pilot's seat and through his legs, but this was not a real problem. There were three basic problems with the P-39:
1) The engine was an Allison V-1710. There was nothing inherently wrong with the Allison (there were a few issues that got fixed over time), but the original specification was as an engine for late 1920's airships (dirigibles). As a result, it was specified with a single-stage supercharger. This meant that the engine performed quite well up to about 15,000 - 18,000 feet. The power dropped off pretty fast after that altitude. As a result, the P-39 was not a high-altitude fighter, making it unsuited to higher-altitude conflicts, like in Europe. It didn't have that problem in the Pacific, Mediterranean, or CBI, although it wasn't exactly on anyone's list as a favorite fighter for combat missions.
2) The arrangement of the armament was not well-designed, and the center-of-gravity moved aft when the ammunition was used up. This made for tricky handling anywhere near a stall in hard maneuvers, as fighters are prone to using. As a result, the airplane could be made to tumble if it got a bit slow and the pilot pulled hard on the control stick in combat. This was reported during the war, but was never confirmed by wind-tunnel testing until after the war. Generally, the P-39 handled well. But when the ammo was mostly gone, you had to be careful when yanking it around the sky.
3) The P-39 was never envisioned as a high-altitude, long-range fighter. So, it didn't have enough fuel to be used as a bomber escort unless the mission were relatively short.
I summary, the faults above are not unique to the engine-behind-the-pilot, but WERE present in the P-39.
* They COULD have used a 2-stage, supercharged engine or, at least, an engine rated for higher altitudes ... but didn't. The P-40 had the same engine and had the same low-altitude restrictions. The P-38 used the same engine (actually power section), but it had turbochargers and could get to high altitudes and operate effectively there. The P-39 airframe was small, and there was not really room for an effective turbocharger installation. The P-63 was similar to the P-39, but was larger and HAD room for another engine boost stage. That's another story altogether.
* The movement of the CG aft as ammunition was used up could have been fixed or at least addressed, but was never anticipated for some reason. I blame that squarely on design. The placement of the center-of-gravity at all extremes SHOULD have been anticipated before the first flight. The P-40 didn't have this issue. Neither did the P-38.
* Last, the short range was due to lack of vision when the specifications were drawn up. They COULD have made room for more fuel, had it been asked for. When I say "made room," I mean in the design stage, not added on after the aircraft was built.
While the P-39 was not a BAD fighter, neither was it a top-notch fighter as we used it. The Soviet Union was sent P-39s and used them to great advantage in low-altitude, ground-support war operations ... it was our design, but the Soviets liked it better than we did. Go figure.
