The SharePoint Online Management PowerShell commandlets are not throttle (throttling) aware. Microsoft recommends handling throttling via the following article. https://github.com/SharePoint/PnP/tree/dev/Samples/Core.Throttling Unfortunately, Microsoft's own PowerShell commandlets for SharePoint Online do not implement these recommendations. Customers are getting themselves and their scripts throttled due to the lack of this implementation (option parameter on commandlets?) and lack of notification of this potential issue. It's not realistic to direct everyone to write CSOM. Plenty of savvy administrators can write PowerShell, but not CSOM.