Even after cleaning a toilet, it may still emit unpleasant odors due to a few reasons. One common cause is a buildup of bacteria in the toilet bowl, which can cause lingering smells even after cleaning. Another cause may be a blockage or malfunction in the toilet's plumbing, which can lead to sewage backup and odors. To address these issues, use a toilet bowl cleaner specifically designed to eliminate bacteria and consider calling a plumber to inspect your toilet's plumbing.