It is a product of the manufacturing process.
Dont know for sure about that one but where two oil ways need to join Yamaha drilled a connecting hole from the outside of the case. The hole is then plugged and sealed with some sort of epoxy.
Have a look at the front of the lower case to see where the rod oil squirter holes are drilled , same deal.
If the hole is not sealed find a ball bearing that fits and knock it into the hole then use epoxy on top to seal.