Can the phrase "not comparable" be used in a negative context?
For example, if someone says the latest pirates movie is not comparable to the previous versions, can it mean it is so bad?
I don't know how bad it would mean, but the meaning when you are speaking will depend upon your voice modulation, facial expression and overall body language. For example, An accentuated 'not comparable' with a disappointing or disgusting look may imply its inferiority.
In written form, the meaning will depend upon the overall write-up. If you go on to praise the film in your next sentences, then 'not comparable', here, is used in superlative context. Eg:
As a stand alone written statement, It can be perplexing to the reader.
Yes. "Not comparable" means "cannot be compared". By itself, it suggests neither positive nor negative. There would need to be contextual clues.
"The latest Pirate's movie is not comparable to the previous movies" could mean "because the new one is so bad" or "because the new one is so much better." Or the reason could be something else entirely.
Note that the single word "incomparable" is often used instead of "not comparable".