In issue #1463 it was resolved that <percentage> values never resolve to <number> values when used in calc(). Though the change made to the spec. isn't as clear as @tabatkins' description in the issue.
There it was said that the problem is that calc(1% * 1%) would be valid for opacity (as percentages resolve to <number>s, while it is invalid in width (as it would resolve to length²).

Furthermore, it missed that the definition of percentage values still allows combinations of <number> and <percentage> values in calc() saying

In cases where a <percentage> can represent the same quantity as a dimension or number in the same component value position, and can therefore be combined with them in a calc() expression…

This sentence should be rephrased, so that it's clear that <percentage> + <number> combinations are invalid within calc().

Sebastian