NPM raises an alert if end to end latency between source and destination crosses the threshold for any path between them. Some networks have multiple paths connecting the same source and destination. NPM raises an alert is any path is unhealthy. The loss and latency seen in the graphs is the average value for all the paths, hence it may not show the exact value of a single path. To understand where the threshold has been breached, look for the "SubType" column in the alert. If the issue is caused by a path the SubType value will be NetworkPath (for Performance Monitor tests), EndpointPath (for Service Connectivity Monitor tests) and ExpressRoutePath (for ExpressRotue Monitor tests).
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