Harmon has a point but is that is only half of it.
You can get trapped into 1 of 2 things with a dot. Over aiming or thinking the dot gives you a license not to aim.
It does take some time to get used to it, but the best remedy to what you are feeling now is practice. Shoot 10,000 rounds through it and your body will figure out what it needs to do to shoot with a dot.
What you mentioned about the dot showing you all your mistakes is very true, which is one of the reasons I think a red dot sight is the best tool for a shooter. Don't forget though that the dot doesn't have to be still to make the shot. The great thing about a dot is it gives you immediate feedback to whether or not you can break the shot when not everything is perfect.