Duplicati has recently extended its filtering system to include OS-specific filters, but you have to turn them on.
Where are the “Default Filters” documented
This might help some with complaining files. I suspect that tuning will happen as more experience is obtained.
Other things to reduce complaints are to run with more privilege, such as Administrator group or as a service.
–snapshot-policy can use VSS to read locked files, but VSS doesn’t guarantee a file is consistent at that time.