Is it appropriate to mention lack of expertise in certain area as limitation for master's thesis?
Rather than describing this as a limitation, I would present this as an area for future research. For example, 


  Machine learning methods X and Y produced promising results for predictive modeling. An area for future research would be to optimize these as well as explore methods, a, b, and c.


and then build upon this with details to be an appropriate length (probably a paragraph or two).