While designing the QR Code, if you uploaded the logo in PNG or JPG format then the format of the logo will remain the same even in the vector export. This is why only the logo will pixelate when the size of the logo is increased.
To avoid this, upload your logo in SVG format. This will ensure that the logo does not pixelate when the size is increased.
Tip: If you upload your logo in SVG format, you can edit the color of the logo as well.