Sure plenty, from both inside the service and outside. A few stick out just on the Naval side of things in the run up and during WW2.

The Vought F4U Corsair sticks out because it suffered many critiques similar to the various versions of the F-35. It wasnt maneuverable enough, had poor flight characteristics, was trying to cram too many new things into one aircraft, was too much of a compromised design to be useful, and suffered delays due to the fundamentally nature of the project.

It started life as an in house project in 1938 in response to a Navy RFP for a high speed, long range, well armed fighter bomber for carriers. The Navy officially ordered 600 of the birds 3 years later in June 1941. And it would be another year before the first production aircraft was delivered in July 1942. From there carrier quantifications that fall caused the Navy to be so disgusted they took an almost unprecedented step. They essentially washed their hands fo the project, deciding it just wasnt worth it to try to use the iarcraft as a carrier fighter, allowing the Marines, and British to take delivery of many of the Corsairs for use ashore, or for the Fleet Air Arm to try them on British carriers.

The Navy instead opted for the Grumman F6F Hellcat which had first been toyed with in house for the same RFP. Begun as simply an incremental improvement over the F4F, early feedback from combat pilots added t the refinement and it was able to enter service very quickly in early 1943. The first carrier born Corsairs in the USN then would not show up until early 1944, 2 years after had been hoped for and at a point when the balance of power had already radically shifted thanks to other naval aircraft, and of course Corsairs ashore.

We can also look to the F4F as an aircraft that got slammed by men in the service for compromising the design for what they saw as dumb decisions from higher authority. Notably the war began with the Navy flying the F4F-3, a version with 4 guns and no folding wings, which limited the number that could be carried on a ship. The F4F-4 then would fix that problem with folding wings, but at the cost of extra weight and a reduced ammo load. Pilots could mostly live with that as it meant more fighters per carrier. But they also went from 4 to 6 guns, adding more weight and reducing the per gun ammo count. This was a move mostly requested by the British as they wanted the extra lead per salvo to take down more rugged German and Italian aircraft vs the more fragile IJN planes. The US fighter pilots were less than pleased and many a bitter memo and letter was sent back and forth. And it should be noted late war versions of the Wildcat that were produced by GM for use on Escort Carriers did go back to 4 guns!

The SBC2 Helldiver was one last plagued program. Meant as a larger more capable replacement to the SBD Dauntless as a carrier dive bomber it was begun well before the war, with the first flight being in December 1940 with an order for several hundred already placed. But over 800 changes demanded by the Navy, or required for aerodynamic or ergonomic needs meant the program just couldnt get a working plane off the line. Congress even took note with the Truman Committee examining the issues, faulting Curtiss Aircraft heavily, and took them to task for this and several other production quality issues in their other aviation facilities, the company would actually get out of the aircraft design field all together in 1948. The aircraft even when finished wasnt initially well liked, the SBD had been a kind and forgiving plane, while the SBC2 was something of an Ensign Killer when it came to mastering carrier landings, and it would not see combat till November of 1943.

None were even adjusted for inflation near the cost of the F-35, but especially the Corsair and Helldiver represented programs that were going to win no awards for being well run at least as seen at the time.

Other far more expensive projects in WW2 also had their share of design critiques. Early B-29's were of course the most expensive bomber ever fielded to that time,a nd their engines had a nasty habit of spontaneous combustion! While into the jet age plenty of new projects have been written off as needlessly complex, hideously expensive, boondoggles. Hell if all we care about is teething problems the F-16(begun as a light weight tactical fighter to be fair) earned the nickname of 'lawn dart' for its high rate of engine failures. Though the evolution in how the US develops aircraft philosophically has also changed. Now it is far more preferred to get as close to the 'mature' design as possible and then send it to the operational force. In decades past you might see the aircraft get to a point where it can sorta mostly fly and fight, with relatively simple or basic avionics and weapons, slap an A variant on the design and ship it out. then work on a better more complete version for 2 years that you really wanted to from the start and send it out as the B or C version until its time for a new project or the money runs out.