Вот что нам говорит Википедия про F-104G в Германии:

The introduction of a highly technical aircraft type to a newly reformed air force was fraught with problems. Many pilots and ground crew had settled into civilian jobs after World War II and had not kept pace with developments, with pilots being sent on short "refresher" courses in slow and benign-handling first generation jet aircraft. Ground crew were similarly employed with minimal training and experience. Operating in poor North West European weather conditions (vastly unlike the fair weather training conditions at Luke AFB in Arizona) and flying at high speed and low level over hilly terrain, a great many accidents were attributed to controlled flight into terrain or water, (CFIT). Luftwaffe losses totaled 110 pilots.

В двух словах.
Летчики были не достаточно подготовлегны к сложным самолетам 2-го поколения, погодные условия северо-западной Европы тоже не способствовали, а поскольку летали быстро и низко над холмистой поверхностью, то основной причиной катастроф явилось управляемое падение в землю или в воду. Всего Люфтваффе потеряли 110 летчиков.