The problem the Germans had came down to lack of training and flying the F-104 in a role significantly different from what it was originally designed for.

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The F-104 was designed as a short-ranged point-defense interceptor and air superiority fighter. Both conceptually and performance-wise, it was very similar to the MiG-21. A key feature of the F-104's design was its wings, which took a different approach to get the kind of high-speed performance other aircraft used delta and swept wings for. The F-104's wings were effectively the ideal supersonic wing - small, straight wings that were very simple, sharp-edged, and very thin. The leading and trailing edges of the F-104 were notoriously sharp enough so as to require safety coverings for ground crews, and the wings themselves had no twist (unusual for the time) and used a simple 3.36% thickness biconvex airfoil, giving the wing a maximum thickness of just over 5 inches at the root. From the supersonic aerodynamicist's perspective, this is great - the F-104's wing is the ideal design for supersonic flight.

But there were massive tradeoffs in more traditional flight regimes. Small wings lead to high wing loading, which in turn requires higher takeoff speeds and longer takeoff rolls, and is generally detrimental to low-speed agility. For the record, the F-104's wing loading wasn't unusually high for its contemporaries (The F-105 had a similar wing loading and the F-101 was significantly higher), but the new roles the fighter took on would exacerbate the downsides. The wing optimized for supersonic flight also hurt. While a sharp-edged thin symmetrical airfoil is optimal for supersonic flight, the opposite is the case for subsonic flight. Sharp leading edges and thin airfoils suffer from flow separation at lower speeds and angles of attack than more traditional airfoils. Combine that with high wing loading, and you get a situation where aggressive low-speed maneuvering can be very dangerous.

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Unfortunately, the F-104G that the West Germans had was designed for operations well outside the F-104's originally designed role. Rather than a high-speed, high altitude air superiority fighter, the F-104G was a heavily modified variant intended to replace the F-84F in the tactical nuclear strike role. In particular, this role entailed flying at very low levels under enemy radar and "toss-bombing" a gravity bomb onto a target. It featured an overall strengthened airframe and improvements such as an enlarged vertical tail and larger flaps to improve the design for this new mission profile, but a lot of the inherent shortcomings of the design (and of supersonic jets in general) lingered.

And here's where the Germans come in. The West German Air Force was fresh and very new to supersonic aircraft. Despite their reputation in the Second World War, most of their wartime experience was either retired, promoted to leadership roles, or no longer relevant in the jet age. The F-104G was Germany's first supersonic jet in an air force that was only recently reestablished and heavily reliant on conscription. Training standards for ground crews that may have been adequate simpler and more traditional aircraft were dangerous for something as advanced as the F-104G, and pilots used to flying more forgiving aircraft like the F-84F weren't going to have much room to make mistakes on the F-104G. The mission profile and conditions in Europe only made things more dangerous, as it entailed lots of low-level flying in hilly terrain in often poor weather.

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Ultimately the blame given by leadership for the high accident rate seems to have fallen on inadequate training coupled with the unforgiving nature of the F-104 in general. The F-104 did have an unusually high accident rate even in US service, but its poor reputation in German service seems to have come from a combination of several high-profile accidents, bad blood over the Lockheed Bribery Scandal, and inexperience with such an advanced new design. With other operators, the accident rate remained high (the Canadians lost an even larger proportion of their fleet than the Germans), but the aircraft was popular with some and even quite effective in exercises. It actually remained in service surprisingly long given its infamy - Canada retired its CF-104s in 1987, and Italy didn't retire its last F-104 until 2004.