It is possible that there is a delay in events becoming available for query in the Graph API due to a variety of factors such as resource contention, scaling events, or other issues that may be out of your control. The fact that the number of events that appear in the delayed queries varies widely, from 0.01% to up to 20%, over a 24-hour period seems to suggest that there may be some latency in the API.
To help identify the cause of this latency, you may want to consider monitoring the performance of your API queries over time. This could involve measuring the time it takes for events to become available for query and tracking any trends or patterns that emerge. You may also want to consider working with Microsoft support to troubleshoot the issue and identify any potential solutions.
In the meantime, one potential workaround could be to increase the time delay before querying a given time range. While this may not guarantee that you capture all events, it could help ensure that you capture more events over time. Another option could be to use a different method for ingesting data, such as real-time streaming, if that is available in the Graph API.
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