I feel your pain, I had the same exact thing happen! I saw a rabbit and squirrel in the yard lately but I'm not sure what did it. I had four and three were eaten completely and the fourth is half gone. Tomatoes, green beans and beets are all around hen and those are fine. It's weird. Next year I'll have to cage them. First time gardening so you live and learn as you go.

Soybeans are like candy to herbivores... as has been mentioned, they will pass up everything else in the garden, then eat the soybeans to the bare stems. That includes rabbits, deer, and the occasional ground hog.

I never needed fencing (except around the corn) until I started growing soybeans. There were rabbits running through the garden (as witnessed by their pellet deposits) but I let clover grow in the walk ways, and the rabbits mostly just ate the clover.

If you don't fence out the rabbits (and deer, if you have them) chances are your soybeans will never reach maturity.