'That animal sells' would be "वह जानवर बेचता है" because जानवर is masculine. But in general, you are right that there may be some amount of ambiguity.
The sentence वह जानवर बेचता है, when understood as 'That animal sells' (as in the animal is doing the selling) does sound incomplete though because बेचता doesn't have an object.
If you are intending 'That animal sells' in the way that donuts sell, then you have to use the verb बिकना (to be sold). The sentence would then be वह जानवर बिकता है