If you have these files previously tracked in git, they are already recorded in git’s view of the branch content. Git still knows about the files and will ask you to merge, even if you try and ignore them.
You could have the files forcefully ignored - see Ignore files that have already been committed to a Git repository and specifically this answer on how to use git ls-files
to have all the files that match your newly introduced .gitignore
excluded automatically.
Alternatively, and what seems to me like the better approach in your case – you could use git attributes to describe specific merge strategies for the files. See http://git-scm.com/book/en/Customizing-Git-Git-Attributes#Merge-Strategies
You don’t want to merge the migration files from develop to master, say, you can setup an attribute file like this (under master):
----- migration/.gitattributes ----
* merge=ours