When Filter>Transformations is opened, if any field (I tested Transform) has an existing value from a previous operation, it is immediately applied to the existing glyph.
If one doesn’t happen to notice this, it could cause problems.
I believe the proper operation should be None until a new value is entered or Cancel/OK is clicked.
So, alternatives:
Have a Reset button to reset the fields to zero/default and undo what was just applied might be a solution.
That, however, might create errors so an even better solution might be to have the default behavior of the panel to reset the fields to zero/default when the panel is opened, then have a checkbox inside the panel which would retain values to override that.