Falcon has already addressed the first issue of too many A6Ms. If you get rid of the multiple takeoffs at the beginning of the frame, they met their maximum.
Second, with respect to meeting the minimums: The Axis Orders had sufficient numbers of squadrons assigned to meet the minimum number of D3A. You may not have been around during the creation of the "Kurt" rule, but it basically states that a CIC and side shall not be penalized as long as the CIC planned to meet the minimum/maximum requirements. As several squadrons that were assigned to fly the D3A had a fraction of their commitment level actually show up, the Axis shall not be penalized for their lack of participation. We'll hold those penalties for the squadrons themselves.
Further, the same condition would apply to the Allied side in this case, as they did not meet the minimum number of SBD, once you take away all of the multiple takeoffs. I did not apply a penalty to the Allies for this, so my scoring is consistent.