The Salesforce Reports API comes with certain limitations one of which is that you can only retrieve 2000 rows of data per timestamp. The timestamp here being the date you selected to attribute your data to when you connected the source.
In order to get around this limitation we suggest:
Pick another date when connecting that always exists and is more evenly distributed.
Filter/group the data in the report in your Salesforce UI before connecting it to Funnel to only include the data you need.
Try out the standard Salesforce connectors to see if they can help. The downside of this solution would be that you would need to then join the data in your destination (where you are planning on exporting the data to).
If none of the above seem to solve this, please contact support.