My 4 month old has low grade temp 99-100 rectally and mild retractions. Is recovering from bronchiolitis 1 month ago. Could it be anything else?

Yes. This could be a new process or related to the bronchiolitis. If these retractions are new or worsening then you need to be concerned and see your doctor. The same is true if the fever continues to climb. 101 or higher.
Yes. A tamperature taken rectally may be nomal at 99 to 100, but if your child has retractions, he or she should be seen by a doctor.