This bug was fixed with commit https://github.com/gohugoio/hugo/commit/4b5f743959394d443c4dcaa0ccae21842b51adaf
Also there is an issue https://github.com/tdewolff/minify/issues/238 regarding the default behavior of the minifier and rgba HEX values (for anyone who is interested in tracking it).
Again, a very big thanks to @bep for issuing a fix so quickly. This will be available in the next Hugo release.