In Project Online and SharePoint Online there are various levels of resource usage that can trigger throttling of your service – and potentially blocking completely. A great general article on this topic can be found at https://msdn.microsoft.com/EN-US/library/office/dn889829.aspx – titled How to: Avoid getting throttled or blocked in SharePoint Online.
There is a new SharePoint 2013 throttling mechanism coming into play currently that will suspend workflow instances when it reaches 1000 outbound requests within 24 hours. If a workflow does get suspended, then the reason for suspension will be displayed against the workflow status – so you can check if it was throttling related or some other reason. You can then resume the workflow after the 24h have expired (this starts from the time the instance is created or resumed).
This change is specifically documented at https://support.microsoft.com/en-us/kb/3076399 - SharePoint 2013 workflow throttling and performance in SharePoint Online and Project Online. The example given are very SharePoint centric – and I will be looking to follow up on this post with more details of how this relates directly to Proect Online in terms of instance and scope definitions, as well as how out Project Online specific activities can play into this. We will likely have some samples too – in another KB. So just a heads up at this point – more information will follow – but if you have particularly chatty or loopy workflows you may get throttled!