as long as you have fully drained the oil (both sump & chassis) and allowed enough time for the drain to take place, then filled with the right amount, then if your measurements are confusing, then

after waiting for few minutes, maybe the oil in the frame seeps back down to the bottom of the engine or

you do not have the bike horizontal (you can someties see the top of the oil through the removed filler cap or

your quantities were not correct

I generally never put in the amount in the handbook but a little less, run the bike , check the level , if needed top it up. much easier than taking oil out of an over filled engine