The spatial analysis of young stellar objects (YSOs) has proven very valuable to describe and analyse star-forming regions and to understand the star formation process. This work aims to provide a homogeneous catalogue of small, significant substructures (henceforth NESTs) extracted from the spatial distribution of YSOs in a large, consistent sample of star-forming regions. The catalogue allowed us to explore the relevance of small-scale spatial substructure and discuss the interpretation of NESTs as tracers of star formation activity and remnants of the star formation process. We applied our procedure to consistent catalogues of YSOs to obtain NESTs in a sample of star-forming regions. We applied a photometric classification scheme to obtain the evolutionary stage of YSOs and statistically explore the distribution of Class 0/I objects as a proxy of recent star formation activity. The region sample is diverse (in distance, size, structure, and global evolutionary stage), and we consequently found different structural properties and star formation histories. Most NESTs in regions with relevant recent star formation activity showed even higher levels of activity. Moreover, the proportion of NESTs with more activity than the region average increased with the global level of activity of the region. In approximately half of the regions, we also found significant spans in the evolutionary stages of the NESTs, consistently with gradients and episodes of star formation. The combination of NESTs with a statistical exploration of the star formation history within each region provides robust and powerful insights into the star formation process. Our results support the role of NESTs as pristine remnants of star formation in highly active regions, highlighting the role of fragmentation. The combination of small structures with large-scale spatio-evolutionary patterns suggests hierarchical, prolonged, dynamic, and complex star formation scenarios.