What ACL injury specifcly? A small grade tear? The majority of ACL injuries happens in knee valgus, small knee angle, internal rotation of the femur and under de-acceleration. The valgus collapse would make sense as to why your MCL was affected too. Duck feet certainly wont help, but there are other equally important factors. Besides being a physio myself, I tore my ACL some years ago and had it replaced. Your best bet would be to go get an assesment from a qualified professional. Generally, strenghtening your glut medius, hamstrings and feet, and getting control of your hip rotations with single leg exercises will help. It's all about the quality of the work though.
My feet points outward too when I lay on my back. That is completely normal. As I said, we have different hip anatomy.
So forth. Don't mistake the "abnormal" for not common.
However, what we all share, more or less, is the loose packed or "open packed" position of the hip. Which is about 30* flexion, 30* abduction and some external rotation:
http://www.physio-pedia.com/Hip_Anatomy#Open_Packed_Position It's the position where your ligaments and capsule is most relaxed in the hip, so naturally when you lie down and relax your feet will externally rotate. How much depends on your hip anatomy. It has nothing to do with your hip flexors.
Some hip flexors like the m. sartorious externally rotate the hip, others like the m. tensor fascia latea internally rotate the hip. Iliopsoas will do little either way.
It's all good and well to stretch your hip flexors out. If you want to look for stretching and release techniques, I'd recommend Brent Brookbush on youtube. He knows his anatomy very well. If you want to strengthen your knee and train for injury prevention go to a physio, not Naudi. Even coaches like Joel Seedman have some very good material on foot and knee stability.