That happens all the time. Whatever treatment is used - imiquimod (Aldara), podofilox (Condylox), freezing, trichloroacetic acid, and others - it is common for warts to respond initially and then become resistant. Overall, Aldara is effective in eradicating warts about 60-70% of the time. Check with the provider who prescribed your treatment; the first thing is to be certain you really have persistent wart tissue and not just a heaped up scar. But assuming it's a wart, you'll need to try one of the other treatments.
Good luck-- HHH, MD