Attached is a simple part with two oddities.
1) The hole pictured is "Up to next", but it did not stop at next and formed a flat on the opposite side. This is weird for two reasons. First why did it not stop at the next object which would be the face and then why is it showing a flat bottom instead of a drill point if it's actually going to the opposite side? Up to surface works properly but then calls a depth out on the drawing. Up to next is the only option that says "thru" on the drawing. Not a big deal to change any of the callouts just an oddity if I'm wondering if I'm doing something wrong.
2) I have an advanced hole on another surface. The hole works fine. However if I pick the point in the sketch and constrain it horizontally to the mid point of the line next to it, it adds another hole.
Dimensioned
Constrained to the mid point of the line
For problem #1, you can make the part behave by making the slit cut a separate feature and putting it after the hole wizard hole.
The hole wizard has some sort of bug that is causing problems. Strange thing is that the hole wizard sketch gets the depth correct, but then something comes along and mucks it up: