mongodump download collections only if changed
As at MongoDB 4.0, collection metadata doesn't include a last modified timestamp and there is no record of when mongodump last ran (or what collections were dumped).

You could write a custom script if you have a means of identifying relevant changes in your deployment since your last backup timestamp, but there are some potentially tricky aspects such as documents that have been removed.

One approach would be to use Change Streams to keep track of relevant collections that have changed since the last backup time, but this would require a replica set deployment. It is definitely possible to configure a single member replica set deployment if that suits your requirements.

It would be more ideal to use a supported backup method if your actual goal is incremental backups rather than per-collection mongodump.