Guns had to be left behind, and part of the dragoons were forced to serve dismounted, because of a shortage of horses. This was an indicator that Napoleon actually intended to invade England if he got the chance. He was not planning on a war against Austria. When the Austrians invaded Bavaria without a declaration of war but demanding that Bavaria put her army in the field to support the Austrians, Napoleon turned for the Channel.
And there were logistical problems, especially after the French crossed the Rhine. And it was because of those problems that Napoleon reformed his logistical system which included creating the military supply train in 1807. Interestingly, the French still didn't have ammunition supply problems in 1805. Capturing Austrian depots intact was indeed a windfall and clearly demonstrates the incompetence of the Austrian commanders.