I'm getting a bunny and didn't know if the smell of a cat would freak her out even if they became friends or if they could get each other sick that way even if i cleaned it out or if it's okay in general?
Your cat and rabbit can share the same carrier, unless someone is ill it does not need to be cleaned between. With proper introductions cats and rabbits can become very good friends. The can share everything, except food (which neither is likely to like of the others) and they should not share litter boxes (easier to say than enforce)
Depending on the relationship your cat and rabbit form, they may be able to share the carrier at the same time. For stressful events like trips to the vet, they may benefit from having their friend along on the trip.
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