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Example:
This is the original image:
I then use Effects > Distort & Transform > Transform and set it to reflect.
and this is what I see.
If I put my cursor over it, it shows that it is still there and I can click on it to highlight it again.
This is driving me crazy.
What am I doing or what setting is wrong?
If you don't wish to have a live effect which can be further edited or adjusted, don't use the Effects menu. Use Object > Transform > Reflect.
When live effects are used, the original objects remain in tact and their appearance is merely altered by the effect. In this case the original circle is still there, but the effect is telling the circle to appear as if it we reflected to the right.
This is normal and it's not new. This is how effect have always worked.
Set the number of copies to 1. See screenshot below. If you have it set to 0 (the default), it will make no copies and simply apply the transform effect. By the way, this is Illustrator's normal behaviour, nothing new.
Note: If you want to bake in the effect so you get two real objects, select the object with the transform effect, and click Object > Expand Appearance
