We have a remote event receiver associated to a list and hooked on all events there. When you update any list item using OOB SharePoint page, the event receiver is executed; a web service which is taking care of the afterward actions works nicely. However when you update item use CSOM code e.g. in simple console application, nothing happens. The event receiver is not called at all. I found this issue on both SP 2013 and 2016.
I will not post any code while it is irrelevant: item is updated using standard approach and values are actually changed in the list item, only the event receiver is not fired. To put it simply: item updated manually from site -> event receiver fired item updated via CSOM -> event receiver not fired.
I remember similar issue on SharePoint 2010 when using server side code and system account. Could it be that behind the scene web service called by CSOM (e.g. list.asmx) is using system account to make changes as well? It's just hypothesis...