Changes in major revision
In addition to making changes according to the reviewers' comments, you may also make other corrections and changes that improve the quality of the paper. However, you should indicate to both the editors and the reviewers that you have made such changes, and explain why they have been made. Given that it's a major revision, the paper would go back to the reviewers anyway, so it makes sense to correct everything possible. 

As a caveat, however, such corrections should not be made in an attempt to skirt around flaws raised by the reviewers. I recently reviewed a manuscript where there were several anomalies in the data, and I mentioned these in my review. The authors completely removed the offending data, and replaced them with new results that better "fit" their conclusions. Such behavior is not acceptable, as they did not explain why the previous results were wrong; they just replaced them.