Are there many tiny files? They may take 4KiB of space each even though they're less than a KiB big (https://en.wikipedia.org/wiki/Disk_sector).

On a SanDisk portable SSD I own, the cluster size is even 4MiB. If you put a node modules directory in there with thousands of tiny files, it can "take up" several GiB of space.

This can be an important reason to enable compression (on some file systems it “solves” the problem) and why virtual machine file format can be important.