Yes, "I am seeing X" most often means "I am dating X."
Phrases like "I am seeing..." and "You are seeing..." are also used in visualizations and hypnosis. Fortune tellers and seers (never mind whether they're for real or not...) may also use "I am seeing..."
And, as rBhr5 says, "I am seeing / You are seeing..." can also used in sentences like this. To my own (AmE) ear, this usage is less common than "I/You see / can see..." but that may be regional or what I'm used to compared to what rBhr5 is used to. I will add it, if other members of the team are comfortable with it.
UPDATE 11 Sep 2019----- After considering it at some length, the course team has determined that the present continuous is not a good fit here and will not be accepted.
Yes, it can certainly mean that, and probably most often it does. But it can also in some cases be literally be another form of the present tense of 'to see' (continuous present). It depends on context and it's a bit nuanced. In relation to the exercise here, if someone said 'Oh, look, there's a duck over there,' and it was really a goose, I might reply, 'You're not seeing a duck but a goose.' Or 'No, that's not a duck you're seeing.' Or I might ask, 'Can you see that hen over there?' and my friend might reply, 'No, I'm not seeing a hen, only an egg.' In this case, they could equally say 'No, I can't see a hen, only an egg'. It's a matter of usage - in some contexts, it will just feel more natural. In this particular case, 'You do not see a duck but a goose' doesn't feel entirely natural to me, but not every native English speaker may feel the same way. It may be because where I live we don't say 'I see/I don't see' much anyway, but 'I can see/I can't see' instead, but that doesn't work in this case.
Minor observation: I translated as 'You don't see a duck, but a goose', mistakenly placing the comma, and the translation is flagged as wrong, which I find a bit hard. Wouldn't it make more sense to count that as a mere typo? Or does that comma actually change the sense of the English sentence? I'm not a native English speaker so I might be missing something here.