The introduction of the Merlin Mustang was a new thing for the 8th AF, with Packard just begining the production of 2-stage V1650s in Spring 1943. As a new outift, it will come with more or less a number of issues. That was true for P-47 (P-47B was unfit for war, the engine problems persisted until mid-1943 with P-47C and D, again engine problems with M), F4U (both engine and airframe, not just for carrier service), P-38 (host of the problems with engines' installation, most notably in the P-38J, insufficient heating prior spring of 1944 when installation of second generator allowed for a redesign of the cockpit heating sytem). P-40 in 1941 with restricted engine power.
Basically everytime the design, either airframe or engine or both, was pushing forwar it encountered issues, some designs (and the design staff) being better in overcoming the issues than another. The fact still stand that Merlin Mustang ranged far and wide against German and other Axis targets, with the unprecedented range and performance - just what and when was needed, even if we account the P-38 history. This, added to the wordwide use of the Merlin will still mean plenty for anyone.
If we talk post-war pistons, let's recall that V-1710 powered P-82 were never as reliable nor as performing as V-1650 powered P-82s.