THere are probably quite a few. Here are some quick ones I noticed.
-The obvious first, when Hyde is around Jekyll is absent (also the other way around).
-Once again, Mr. Enfield and Mr. Utterson are walking by the mysterious door. Through one of the windows, Utterson spots Dr. Jekyll, whom he has not seen for weeks. Utterson calls to Jekyll and tells him he should get outside more. Jekyll replies that he wishes he could, but doesn't dare. As he finishes his sentence, his smile disappears from his face and a look of utter terror takes over. It appears as though Jekyll suffers some kind of seizure. Enfield and Utterson only briefly saw the pain in Jekyll's face before he quickly shut the window, but are both appalled. They walk on without speaking of the incident.
-Utterson and Poole approach Jekyll's cabinet door in the laboratory, and Poole announces that Utterson is asking to see Dr. Jekyll. A voice that does not sound like Jekyll calls out to say that he will not see anyone. Poole returns to where Utterson was hiding and asks if the voice sounded like Jekyll. Utterson agrees that, "It seems much changed."