The dividers don't go all the way to the top of the housing, just high enough to keep the right oil depth for each section. Anything over that runs into the back compartment. The gears move the oil when everything is turning, so it probably got flung in the back.

Each shift fork is held to its shift rail by two bolts, so if that is where it is from you have a shift fork hanging on by one bolt. The fork fits the contour of the rail, which is round, so if one bolt is tight, it will stay in place. There's also the possibility that someone else worked on it, dropped the bolt, and did take the time or forgot to fish out that bolt. It wouldn't be the first time I came across a transmission that was repaired but wasn't cleaned out.