We log every request that you make to your site. For e.g, if you open the General Ledger Report in your site and it takes 2 seconds for the report to generate, we log that time. This is the CPU usage time. This time will add up as you use your site.
Now, based on the plan you chose, we will check if the total CPU usage time is used up, if it is we will drop the request and all the subsequent requests. If this is happening frequently to your site, it is an indication that you should switch to a higher plan.