A drug substance, (8-(2,6-dichlorobenzoyl-amino)-3-hydroxymethyl-2-trifluoromethylimidazo [1,2-a] pyridine (named BPPI)), developed for osteoporosis treatment, has two crystal polymorphs: an unstable B01-form and a stable B02-form. In the early stage of development, only the B01-form was always obtained from an ethanol/water solution. However, after improvements in purity of BPPI, only the B02-form was obtained. Four major impurities incorporated in the B01-form are identified and 4 analogues of BPPI are separately synthesized. The inhibitory effects on the solvent-mediated transformation of the B01-form to the B02-form are examined to explain the disappearance of the B01-form and the new appearance of the B02-form. As a result, it is found that the dimer of BPPI, which was a by-product of the last reaction of BPPI synthesis, had inhibited nucleation of the B02-form crystals. 0.107 mg/mL of dimer completely inhibited the transformation of the B01-form. The inhibitory effect of the dimer on the nucleation of the B02-form is discussed by focusing on the failure of two intermolecular hydrogen bondings that should be formed in the B02-form crystal.