If a user answers with a meaning in place of a reading or vice versa, then the UI should provide a warning and give them a chance to correct it rather than counting it as wrong. There is very little reason to punish the user just because they confused the two.
For example, when reviewing the reading for 天, if the user puts sky, then it should recognized they accidently answered with the meaning and warn the user instead of treating it as a failed review.