align_image_stack can struggle when the images differ by more than simple focus changes. In your case, handheld macro shots likely include translation, rotation, perspective/parallax changes, and possibly subject/background movement. Those differences can confuse automatic alignment, especially if the background moves differently from the subject.

A few practical points:

• For focus stacking, a tripod is strongly preferred.
• If possible, decide the goal first: focus stacking, removing objects, HDR, etc., because alignment strategy differs.
• Avoid using -t here; it reduces control-point accuracy.
• Use -p to save a .pto project and inspect the control points in Hugin, or use Hugin directly.
• In Hugin, generate control points, then delete points on the background so only the main subject is used for alignment.
• If fusing in Hugin, use exposure fusion settings appropriate for focus stacking, such as contrast-only weighting.

So the main issue is not that the software is broken; it’s that the image set is too inconsistent for fully automatic alignment. Manual control of control points in Hugin gives you a better chance, but if the subject itself moved, even that may not produce a useful stack.