So I finally found the answer after searching for a year!

First identify which drive letter the USB stick has received from the
kernel

sudo parted --list
For example this USB drive is on Device Serial Disk h: (/dev/sdh)

Model: KINGSTON DataTraveler G3 (scsi) Schijf /dev/sdh: 4001MB
Use the information to wipe all the partition tables and data from the drive

⚠ WARNING THIS NEXT STEP WILL DESTROY ALL DATA ON THE DRIVE ⚠

sudo wipefs --all /dev/sdX
Make sure that you have chosen the correct USB stick for the value of X so you 
don't accidentally wipe your harddrive/SSD

Warning message

"The driver descriptor says the physical block size is 2048 bytes, but
Linux says that it is 512 bytes." Means that the dd command in behind
the nice GUI forgot to specify the bs=2048 option.

Background

It's not that the unused space is wasted. The USB disk has been
corrupted by USB Startup Disk Creator. For some reason USB Startup Disk
Creator has become CD-ROM creator. It writes your USB-Stick to iso9660
format which is only intended for CD-ROM's. Since new computers don't
come with CD-ROM players or writers anymore this is a regression bug

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https://bugs.launchpad.net/bugs/1708881

Title:
  USB Stick corrupted - The driver descriptor says the physical block
  size is 2048 bytes

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