The misalignment between a stated research gap and the corresponding research proposal was among the most common and consequential errors in academic research design, yet it received relatively little systematic attention in research methodology instruction. When researchers identified a gap in the literature but then design a study that does not substantively address that gap or when the research gap was so broadly or vaguely articulated that it cannot coherently motivate any specific study; the entire scholarly enterprise was compromised: the research questions become directionless, the methodology becomes unjustifiable, and the contribution of findings becomes unclear. This qualitative study explored how postgraduate students and academic supervisors in Ugandan universities understand, experience, and attempt to navigate the challenge of gap-proposal alignment. Drawing on in-depth interviews with 34 participants including 22 postgraduate students and 12 academic supervisors at five Ugandan universities the study generated rich phenomenological accounts of confusion, frustration, breakthrough, and development around this methodological challenge. Findings revealed that gap-proposal misalignment is nearly universal among early-stage postgraduate students, was frequently not diagnosed until late in the proposal development process, and was experienced by both students and supervisors as one of the most difficult intellectual challenges in graduate education. The study proposed a practical conceptual framework-the Gap-Purpose-Questions (GPQ) alignment model grounded in participants' accounts of what helped them achieve coherence, and illustrates its application through three detailed case examples drawn from Ugandan research contexts.