How to interpret Azure SQL QueryStore Query Performance Insight
It’s possible that CPU spike was short, let’s say for 5 minutes reached 90%. Each bar represents a query that runs for 1 hour.
So, in this case, you will see, one bar taking 5/60 * 90% ~ 7.5% 

QPI will show you most significant queries in the observed interval, and time grain is one hour.  If query spiked and its significance is not big enough to get into TOP 20, it won’t be shown.

You can change the granularity of monitoring chart (DB Blade, Monitoring Chart, "Edit chart") to be 1 minutes and check if the spike was short. 

Hope it helps,
Andrejs