Genome-scale datasets have increased phylogenetic resolution across insects, but they have also exposed persistent disagreement among loci, gene trees and genomic regions. Such discordance is often treated as an analytical defect to be filtered, down-weighted or overwhelmed by additional data. This perspective argues that this response is incomplete. In rapidly diversifying insect lineages, conflict can instead record incomplete lineage sorting, introgression, gene duplication and loss, or heterogeneous histories within genomic regions, although the same observable patterns may also arise from gene-tree estimation error, model misspecification, alignment problems, locus construction or contamination. We therefore distinguish observed discordance from explanations for discordance and from the stronger inference of species history. Evidence from aphids, bumblebees, drosophilids, butterflies, dragonflies, damselflies and other insect groups shows that genuine biological conflict can persist in large phylogenomic datasets, whereas methodological studies demonstrate that apparently convincing conflict may also be analytical. The central proposal is consequently not to privilege biological explanations, but to treat discordance as an inferential object requiring explicit validation. A staged interpretation of marker conflict can preserve biological information while reducing premature mechanistic attribution, indiscriminate filtering and unsupported taxonomic conclusions.
