If I was explaining something to someone and they told me ' I see what you're saying...'
Does that mean that they agree / disagree or they are neurtral- Is it like saying ' I see'
It means they understand the point you are trying to make, although they don't necessarily agree with it. In other words, your argument has merit, but it's not enough to convince the other person.
Usually, we expect that phrase to be followed by "...but...".