It is not clear what problem you are seeing.

[sitifan]

It is not clear what problem you are seeing. (my bold)
In the above sentence, what does "see" mean when used in the present progressive tense?

 

[emsr2d2]

It means what it usually does in "I can see a problem". It simply means that you have spotted (identified) a problem. In your sentence, it means "It's not clear what the problem that have identified is".

 

[sitifan]

What's the difference in meaning between the sentences below?
1. It is not clear what problem you are seeing.
2. It is not clear what problem you see.
3. It is not clear what problem you can see.

 

[Tarheel]

Perhaps:

It's not clear what problem you are seeing. I don't see a problem there.

Or:

I don't see a problem there.

It's hard for me to understand the sentence itself if I can't imagine a context for it.