Field Marshal Albert Kesselring, shortly after he was appointed the German theater commander in November 1941, lamented the "peacetime working methods" of Italian civilian dockyards. This complaint is echoed in Italian sources, Ferruccio Botti estimated as much as 33 % of the supplies intended to be shipped to North Africa were pilfered. The time it took Italian longshoremen to load cargo ships was the slowest in Europe. This contributed greatly to the logistical shortfalls of the Afrika Korps and their Italian allies in North Africa.
Civilian workers in Italy were also under civilian jurisdiction and it was not until the end of May 1943 that Commando Supremo secured the militarization of port workers. This was weeks after the Axis lost North Africa, making this measure superfluous.
Sources: Ferruccio Botti "Strategia e logistica in un'ottica interforze" in "L'Italia in Guerra Il terzo anno-1942" edited by Rainero and Biagini
"The memoirs of Field Marshal Kesselring" by Albert Kesselring

While Rommel may have committed small strategic mistakes in the Battles of Alam el Halfa and El Alamein as well as the African campaign in general, these were not monumental enough that they should be considered compromising.

Instead, Rommel's defeat should be blamed on unsolvable supply problems outside of his control. Far too few supplies were allocated to the Afrika Korps by the Axis High Command (In August 1942, Rommel received 13,000 tons of supplies whereas the British received 500,000). His lack of supplies could also have been attributed to British air and naval supremacy. Nonetheless, these persisted throughout the campaign and severely limited the tactical options he was able to undertake on the ground.

Whatever the reason for Rommel's supply deficiency, it cost the Afrika Korps dearly. By the Battle of El Alamein (October 1942), the Allies had a 2 to 1 numerical superiority in both tanks and personnel committed to the African campaign. The Allies also possessed substantial numerical advantages in artillery, antitank guns, and air support in Africa. These are simply overpowering advantages that no single general, no matter how skillful, can be reasonably expected to overcome. Thusly, no general in Rommel's place could have guaranteed victory and it was not the Field Marshal's decisions that spelt his own defeat.

Helpful sources:

Rommel, Erwin. The Rommel Papers. Ed. B. H. Liddell-Hart. Comp. Manfred Rommel. Trans. Paul Findlay. 15th ed. New York: Harcourt, Brace, 1953. Print.

Sears, Stephen W. Desert War in North Africa. 1st ed. New York: American Heritage, 1967. Print.