Two F-35B aircraft fly in formation over Edwards Air Force Base, Calif., in September 2013. Lockheed Martin The US military's fifth-generation fighter is no stranger to controversy.

The F-35, which comes with an estimated $1.5 trillion pricetag over the life of the program, has faced numerous hurdles and delays. Most recently, there have been concerns over its computer systems' vulnerability, and Chinese hackers have possibly stolen classified data related to the project.

The F-35's construction has continued, and it is being manufactured across multiple states and different countries. For better or worse, it's going to be the US and its allies' main warplane for decades to come.

Despite the setbacks, the F-35 program is continuing and the Navy, Marines, and Air Force are all busy testing their version of the aircraft. But just because the military is sticking to the F-35 doesn't mean it isn't acutely aware of the plane's myriad problems.

During the live flight testings in 2014, the Department of Defense's Office of the Director, Operational Test and Evaluation compiled a report on the progress and failures of the F-35 program.

Here are some of the key problems that the Pentagon identified.

Software delays

The Pentagon discovered deficiencies in the plane's Block 2B software system. Block 2B oversees the plane's initial warfare capabilities, like its various data links and live-weapon firing system. The worst deficiencies were found in the Block 2B's navigation and accuracy software aspects. These software problems slowed weapons integration and flight-testing, and with it the entire aircraft's development.

Block 2B also encountered issues with weapon delivery accuracy. The software still had trouble in the use of radar, passive sensors, friend-or-foe identification, and electro-optical targeting.

The 2BS5 software package, which deals with sensors, also continues to run into difficulties. According to the report, "fusion of information from own-ship sensors, as well as fusion of information from off-board sensors is still deficient. The Distributed Aperture System continues to exhibit high false-alarm rates and false target tracks, and poor stability performance, even in later versions of software."

F-35B fuel tank redesign

The F-35B was given a redesigned fuel tank ullage inerting system for the fuel systems simulator – in English, this is the part of the plane that prevents potentially explosive interactions of oxygen and gasses in the aicraft's fuel tanks and intake. Further tests showed that the redesigned system had problems in aircraft integration that would require further hardware and software modifications.

Lightning protection

The fifth Lockheed Martin F-35B Lightning II Short Take Off/Vertical Landing flight test aircraft delivered to the Marine Corps arrives at Naval Air Station (NAS) Patuxent River, Md., Liz Kaszynski/Lockheed Martin

The F-35B did not maintain "residual inerting after flight for the required interval of 12 hours, which is a lightning protection requirement." In other words, the plane would be vulnerable to lightning strike if it were forced to fly twice in a 12-hour span, unless the fuel tanks were frequently "purged" with "external nitrogen."

That's apparently an unacceptable additional layer of maintenance. If a solution is not found, F-35Bs will require the development of alternate lightning protection methods.

Flight control problems

The F-35B encountered difficulties carrying out attacks at certain angles during intense aerial conditions due to a degradation in the flight control system as missions progressed.

Helmet display issues

Onboard testing on the F-35C revealed problems with the helmet, which is designed to display critical information related to the aircraft.

During basic offensive and defensive maneuvers, the conditions negatively effected the display, a problem that could have "the greatest impact in scenarios where a pilot was maneuvering to defeat a missile shot."

Numerous components of the aircraft are unreliable

An F-35B test aircraft completes its 100th flight with Lockheed Martin test pilot David "Doc" Nelson at the controls. Flickr/US Navy

The F-35 has a number of components that require maintenance more frequently than desired.

According to the Pentagon report, all variants have reliability issues with their avionics processors, landing gear tires, thermal management systems, ejection seat assemblies, cockpit display electronics unit, helmet display units, seat survival kits, igniter-spark in the turbine engines, and on-board oxygen generating systems.

The unreliability of these systems increases maintenance time and costs on an already expensive plane.

The Automatic Logistics Information System (ALIS)

ALIS is the IT backbone of the F-35. The software monitors all operations within the aircraft and provides information to pilots and ground personnel about any issues arising within the plane.

According to the report, "ALIS is behind schedule, has several capabilities delayed or deferred to later builds, and has been fielded with deficiencies." Some of these deficiencies include misrepresenting the health of F-35 aircraft. The system, which is brought on board the F-35 in flight, has also gone beyond the approved size, bulk, and weight.