Please help sentences were fhlary

Why is the stem rotting. Cut back because stem was soft and musey when touched. What does black spot mean?

Mrainey, when you speak of the black spot. Are you meaning the center of the larger stem which looks to be the one you pruned?

When you prune, the center of cut branch will usually become concave and brown in color, but will become hard. If the center looks to black and very soft, you will want to keep watch that it is not decaying tissue.
From your photo to date. It looks fine.
The edges of the bark should start to dry and gradually become rounded toward the center.

I have to say, that since using Elmer's Waterproof glue as Laura has shown us. The cut ends heal so much cleaner looking and not as noticeable.

Hope your plant will be fine.
Rick