DOF stacking was not set properly, and/or too many/too few photos.
What were your parameters in the focus settings, and how many shots did you combine?
What I do with such macros is set the focus depth increment to 2mm, set it to "+" bracketing, set into continuous mode, set the focus lock at the closest I can, set EV lock, and fire away.
I take many dozens of shots on the tripod.
When I load them all, I clear out the ones at the beginning of the string of shots (usually none need to go) and any shots after the last good focused part of the object.
From there, I may be left still with 3 dozen shots. I then delete the last two photos in every three shots.
In other words, pictures numbered
xx25,
xx26,
xx27,
xx28,
xx29,
xx30,
xx31,
xx32,
xx33,
xx34,
xx35,
xx36,
xx37,
xx38,
xx39,
xx40...
becomes a list of...
xx25,
xx28,
xx31,
xx34,
xx37,
xx40
...and so on. I do this because I can slim down the shots better if I can actually see the finished results. What I find is that the closer the focus is to the lens, the more narrow the width of what is actually in focus. You will see this, too, with only a few shots worth of practice.
Then you will simply hand pick the shots you wish to combine.
Combining too many shots creates what i refer to a "digital anomalies"; some sort of strange blotches and lighting that effects the sharpest highlights and the edges of the photo. I nearly always find it necessary to crop the outside edge of a photo. Once you learn that, you can plan for it during composition.
Here's a composition I made a few days ago. The idea was to include the landscape at infinity. This was whittled down in the way I described from 48 shots to 16.
