Although the use of an alphanumeric designation system might lead to the assumption that the Department of Defense (DoD)'s Mission Design Series (MDS) follows a logical, sequential order, the reality is often quite the opposite. The designation system often makes a good deal of jumps and skips over whole numbers, leaving gaps like F-22 and F-35. Part of the problem is the DoD often has to deal with an entrenched interest in the form of aerospace firms that have a vested interest in the naming of their products. This was part of the reason why there is no F-19 in the US inventory. Although there was much speculation at the time concerning a stealth aircraft or other black project, Northrop was hoping to market its development of the F-5, then known as the F-5G, as the F-20. The company filed a request with the USAF/DoD for the F-20 designation in 1981. The aviation researcher Andreas Parsch uncovered through a FOIA request from the USAF liaison to the F-5G program to the USAF Standards Branch that conveyed Northrop's desires:

In mid 1981, Northrop Corporation's Intermediate Export Fighter candidate was designated the F-5G. Since that time, the F-5G has incorporated substantial changes in structure, engine and aircraft systems. Northrop Corporation believes these changes would be best reflected by a model designation change from F-5G to F-20A, "Tigershark". Northrop's reason for specifically requesting the model 20 designation is that being an even number series [sic], it would be unique in the foreign market which typically sees odd numbered threat designators (MIG 19; MIG 21; MIG 23).

The USAF/DoD approved this request, and the ill-fated Tigershark received the F-20 designation. Northrop's marketing materials, such as this video asserted that it was a modern aircraft and new start, not a refined byproduct of the 1960s.

But corporate branding and marketing is only one part of the DoD's tendency to jump around with its designations. MDS's avoid the number 13 and there is an unofficial rule skipping this number. The F-14, for example, should have been designated F-13 as per the 1962 common designation system, but was skipped (ironically, Grumman had in WWII proposed the name Tomcat for the F7F nightfighter, but the Navy rejected it because of its implications of "feline promiscuity", but changed its tune with the F-14 and some have noted that three of the top admirals in Navy Air in 1969 were all named Tom). Internal bureaucracies and Congressional funding sometimes also plays a role in skipping. One unsubstantiated, but plausible rumor about the semi-official F-16CJ designation in magazines like Air International was that the USAF was afraid that if they followed the Navy's precedent of designating a SEAD aircraft as a new subtype (the G-model of the F/A-18), it would give the impression they were developing a new F-16 model just when the costs of the JSF were coming under scrutiny. The decision to designate the winner of the JSF competition as F-35 apparently came during the press conference on 26 October 2001 announcing the winner of the competition. Edward C. Aldridge Jr., then Under Secretary of Defense for Acquisitions, Technology and Logistics said that the X-35 would become the F-35. Many at the time expected that the JSF would carry the F-24 designation, but when Lockheed-Martin submitted its request for official MDS from the DoD, the request suggests Aldridge was the impetus behind the use of 35:

It is the program office's desire to designate the JSF as the F-35. This request is consistent with the statement made by the Under Secretary of Defense for Acquistition, Technology and Logistics during the public announcement of the contract award. He said the JSF would be called the F-35. This is also consistent with the X-35 designation of the Lockheed concept demonstration aircraft. The USAF, USMC, and USN variants will have the Series designators of A, B, and C respectively.

Parsch and other commentators on the JSF program have noted that Lockheed-Martin's request for MDD took an unusually high time to be approved, suggesting there was some unease within the DoD of jumping to such a high number (23 to 35).

Of course, black programs and the pervasive need for secrecy have also played their role in this confusion. There are rumors that YF-24 is a designation used by an as-yet classified aircraft. Colonel Joseph A. Lanni has claimed to have flown a "YF-24" in a classified test squadron in the mid-1990s, and while such accounts need to be taken with a huge grain of salt and skepticism, the DoD has developed black aircraft like Tacit Blue (declassified in 1996, ten years after being placed in storage) or the modified UH-60s used in the Bin Laden raid that have escaped the notice of number of informed commentators in the aviation press. There also is a history within the USAF of using designations as cover for a wider project, as exemplified by the F-117. This anomalous designation was both a security measure and a bureaucratic shortcut. According to Paul Crickmore, the term F-117 was a way for the Tonopah pilots to record their flight hours when the Nighthawk was working up its operational readiness without revealing the nature of the low observable plane or its mission. However, there was also an overlap between the Nighthawks with another black USAF operation: the flight testing of Soviet MiGs. These captured aircraft each had a individual century designation, and were distinguished by a letter subtype (eg YF-113B for one of the MiG-23s and YF-113C for one of the MiG-17s). This odd designation was done much for the same reason as the Nighthawk's, it allowed bureaucracy to be served while not giving away details of the program. F-117 was a means to differentiate the new aircraft from these ex-Soviet bloc aircraft. Once the secrecy about the Nighthawk was lifted, the F-117 designation remained as a bureaucratic expedient.

As all of the above indicates, there is no straightforward logic to the MDS process. The system itself evolved in an ecosystem in which bureaucracy, corporate interests, and secrecy comingled so that despite promising clarity, the DoD's alphanumeric MDS system delivers the opposite.