This is a longshot based on the size of the bearings, but Nissan FWD cars used to have problems with their input shaft bearings coming apart due to lack of a pilot bearing. Lots of vibration on the input shaft at high RPM would cause the bearing cages to break apart and eventually the balls to fall out into the bottom of the trans and the input shaft would wobble pretty bad, causing fluid leak at the front seal.
The balls from the bearing were quite a bit larger than what you have pictured, but the shift detent balls that had to come out to split the case were indeed the same size as the ones you have pictured.. (Again, that's a Nissan tranny from the '90s.. but in the end all of these we're talking about are made by Aisin, so it's possible they share some design similarities..
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Regarding the shift detent balls... do all gears "sit and stay" when you shift into each gear? their function is simply to provide some stiffness to hold the shifter in places once you shift into each gear. if your trans likes to pop out of a certain gear too easy, then it's possible one of them has come out for some reason. it's also possible (but unlikely) that the factory dropped one inside the trans during assembly. usually those don't go in until the case is together and the shift rods are in place, so one falling inside the trans doesn't seem likely to me.
then again, I've seen stranger things!