The color of the bars in your workout graph is based on the average effort for that entire minute. Therefore if you are at 91% for 30 seconds and 88% for 30 seconds your average for that minute would be 89.5% and your graph would be yellow.
Your Time in Zones is based on the total amount of time spent in each zone over the course of the workout. Therefore your time in each zone may not be reflected directly in the graph.
An example here is that 17 minutes were spent in the Red Zone over the entire workout but only two minutes averaged above 90%.