Path to mime-type .png's is incorrect

Replacing /themes/contrib/bootstrap/images/ with ../../images/ works in both uncompressed and compressed CSS.

I also suspect (not tested) that the SASS subtheme also has a bug about this as ../../contrib/bootstrap/ looks incorrect to me.

Still broken

For css subtheme there is no 100% working definition as it will depend os specific folder structures.
On scss subthemes a variable is set to allow customizations.
In your case and any other folder structures different from theme's "standard" path should be customized on subtheme's css

I'm sorry, but this is not correct.

In the bootstrap theme you need to replace /themes/contrib/bootstrap/images/icons/application-pdf.png with ../../images/icons/application-pdf.png (relative to the CSS files that references the images) and it works all times with both css aggregation and without.