You may have drawn your substructure with incorrect bond types. The CSD uses a number of conventions for bond types; for example, the six C-C bonds in benzene all have the aromatic bond type, but thiophene is drawn with single and double bonds. In addition, the CCDC is careful to ensure that CSD entries reflect the structural details specified by the original author. Therefore, bonding conventions for a particular substructure may not be consistent throughout the database. In this case, variable bond types should be used to increase the range of possibilities. Indeed the pattern of connected atoms in a substructure is sometimes so distinctive that the Any bond type can be used, at least for initial searches. Alternatively, perhaps you've drawn a different tautomeric form to the authors representation.