I'm just wondering what is the diffence between the three as English is my second language. If someone is talking about your work and said "that was fine" or "that went well" or "that was good" which is the best? Or is there no difference at all?

I would personally prefer to hear "that was good". "That was fine" would be a little bit more disappointing personally, with "that went well" in the middleish

It is difficult to say without knowing the person or context. Some people just think differentely about words. So, when I say a paper was "nice" I mean "that was really satisfying and heart-warming to listen to", but some people might mean "that was average" or even "that was slick."

For me, personally:

"that was fine" = yup, okay, you fulfilled basic requirements, but no great insight / excitement.

"that was good" = one-up from the above, fulfilled basic requirements and a bit more besides / or that was better than might be required. Still room for improvement, though.

"that went well" = that was a success - no slip-ups and a positive outcome.

Also, bear in mind that crusty old-school academics can be notoriously reticent about giving praise. I once had a paper accepted for publication, which my supervisor had said was "fine". Heh.

Hope that helps.