One point on which Tooze has a controversial take is on early war German undermobilization.
This thesis goes along two lines. The first is that the war economy prior to 1942 was marked by inefficiencies: labor productivity went down, economic institutions accused each other of incompetence, the price system did not pressure industrialists to innovate and so on; this was particularly bad in 40-41, a period for which footnotes speak of "egotism and incompetence" and of Germany "squandering its armaments advantage". Only under Speer and his rationalization the economy was put in working order. The second is that initially the Reich's leadership wanted to shelter civilians and prior to the "total war" drive of 1943 a large portion of German manpower, plants and capital were still in the civilian sector producing useless consumer goods and the like. Those lines converge to the conclusion that from the very beginning there was a lot of unused capacity which could at any moment, even before Barbarossa, have been unlocked by implementing rationalization and total war.
As soon as the war this entered historiography and remains influential today. I've seen it in Wikipedia, the Paradox Interactive Forums, /k/ and elsewhere. Tooze explicitly bashes the first line and weakens the second.

On the first line:
1)The inefficiencies are called into question. The price system wasn't bad. The apparent productivity decline still appears in revised data (see the third graph in >>29201). The sector which received the greatest number of workers in the France-Barbarossa period was the Luftwaffe, and it is in aerial production that the lag between workers&inputs entering assembly lines and more armaments coming out is the greatest, lasting several months, and this creates the statistical illusion of faltering productivity. In army and naval production output grew much more than the labor force. There was indeed a factor which could harm productivity: the logistical disarray and drafting of workers for Barbarossa, but it was minor. Further, it must also be noted that with the ongoing investment boom the industry wasn't focusing merely on short-term output.
Tooze defends the German war economy in its France-Barbarossa period. It had a clear direction, was coordinated with geopolitical planning and achieved its objectives.
2)The "Speer miracle" was mostly led by factors other than rationalization, mainly the heavy industrial boom and the arrival of foreign workers, so there wasn't that much output to be unlocked by rationalization in the first place, or if there was, Speer couldn't reach it. Milch made a truer rationalization but even most of the extra productivity he got was from his decision to ditch quality for quantity; further, it was easy for Milch in 1942 to outperform 1941, when aerial production stumbled over difficult technological leaps. Not that Speer and Milch did no technocratic reforms, their organizational innovations could've been made earlier and Milch subordinated the big aerial firms.
So Hitler couldn't just appoint Speer or some other technocrat to replace Todt (himself a questionable "miracle-maker") in 1940, seek "rationalization" and get a massive boost.