You need to use two different variables or a cell array of paths:
path1 = ['-I' fullfile(pwd,'tempInclude1')];
path2 = ['-I' fullfile(pwd,'tempInclude2')];
mex('-v',path1,path2,srcFile)
or
ipaths = {['-I' fullfile(pwd,'tempInclude1')], ['-I' fullfile(pwd,'tempInclude2')];}
mex('-v',ipaths{:}, srcFile)
I suggest reading up on how command mode differs from function calling mode. matlab command syntax vs function syntax