As per German Army records, somewhere between 1% and 2% of the total soldiers mobilised became casualties (dead / wounded) during training and exercises (the wounded often came back into combat, still that is a big number). That is a lot of men. Considering 17 million mobilised, that means somewhere around 150000 men. Or approx. 1/3rd of total US casualties (dead) in the War.
Not sure about equipment losses in Training, but somewhere between 2% to 5% of all Luftwaffe aircraft were damaged due to mechanical problems in take-off and landing (during combat), esp. serious in the Bf109 fighters which were difficult for rookies to handle (mainly a late war issue i.e. 1944+), USA too lost about 3% of total equipment during transport and had another 5% or so sunk by U-Boats etc, thus losses of 8-10% in equipment.
There have been several small collisions between planes, tanks and even Ships. I think in the aftermath of the "MIDWAY Battle" the Japanese lost a ship due to "Friendly Fire" and several such incidents happened in the immediate aftermath of D-Day with the 8th Air Force and US Ground Forces.