Supercharging was mature technology at the start of the war while the turbocharger was something quite new. The P-38 used the then radical new General Electric turbocharger (along with the B-17 and P-47) which was quite reliable in itself but the system couldn't tolerate back pressure, which is why the turbine wheel is exposed on the Lightning's turbos on top of the booms - that's where the exhaust comes out.
In any case, the Lightning's many bugs included boost system related issues, but this was mostly due to an ineffective intercooler system in the leading edges that didn't drop the air charge temperature enough. The tetra ethyl lead in the fuel would actually separate out and lower the fuel's octane rating on its way to the cylinders, causing detonation and blown engines. This wasn't the turbo's fault and was mostly fixed by the K and L models with the big chin scoops for the new intercooler. I don't believe the turbocharger unit itself was a major maintenance headache for the P-38.
That's the thing about the Lightning. In its L model form it really was the F-22 of its day. It could outclimb just about anything. With the hydraulically boosted ailerons, at high speed it could out roll single engine fighters in spite of the mass of those booms. With counter-rotating props it had no torque effects with power changes and was jet like as a gun platform. Compressibility problems were mitigated with dive flaps. All the more amazing as a pre-war design. Kelly Johnson really was a mega-genius.
But the turbocharger and intercooler system, with yards of ducting, along with two of everything in the booms, made it very complex and expensive airplane compared to say, a Mustang with its Merlin's simple two speed supercharger, so you could say it was questionable whether it was worth it (there is endless speculation on what a Merlin powered P-38 would've been like). So to answer your question, cost and complexity may have kept a lot of designers from using GE's turbo system, more than reliability.