Not all acquisitions that are acquired during a session are relevant to the BIDS standard. When exporting BIDS to your local drive or to a gear, in the BIDS metadata there is an ignore flag that can be set on every NIFTI image in the session that will tell the BIDS exporter to ignore that file when downloading.
One example would be localizer scans. The BIDS Gear will set an ignore flag on that file if it's labeled with a known non-BIDS classification, like Localizer. However, if another acquisition may not be BIDS relevant but might otherwise look like a BIDS data type, the user can set the metadata value
The BIDS Curation gear will set this flag based on the template it is provided. If this field needs to be set manually, it should be done after BIDS curation gear is run.
The location of that metadata field in the UI is shown below and can be edited there as well.
We also have a collection of webinars on using BIDS and Flywheel.