The primary reason lipids are found in the acid-insoluble fraction, despite not being strictly macromolecules, is because:
The text explains: 'Cell membrane and other membranes are broken into pieces, and form vesicles which are not water soluble. Therefore, these membrane fragments in the form of vesicles get separated along with the acid insoluble pool and hence in the macromolecular fraction. Lipids are not strictly macromolecules.'