It depends a little bit on where the drain plug is and how much might be left in the box. It may be they have a simple suction pump to ensure as much as possible is removed, they use this type of thing for brake fluid replacements. The Honda CVT-F costs ~£40 for each fill +labour +margin. I don't see the error causing damage, but it may be that the Carlube ATF has a different performance characteristic. You'll have the next CVT-F change done in two years time (under standard schedule), if performance is affected you could bring that forward.
--
TG