S1 = regexprep( fileread('level.csv'), '\r?\n.*', ''); %trim off any CR/LF
S2 = regexp( fileread('sequences.csv'), '\r?\n', 'split' ); %break into lines
if isempty(S2{end}); S2(end) = []; end %if final line ended with newline then there is an extra empty line
output = [{S1}; S2]);
fid = fopen('combined.csv', 'wt');
fprintf(fid, '%s\n', output{:});
fclose(fid)
The above does not assume that the line terminators are the same for both files, and assumes that each file might end in a newline but might not. The combined file will be consistent.
In the case where you are certain that level.csv ends in a newline and that the two files are consistent in their line termination, then you can reduce all this to
!copy level.csv+sequences.csv output.csv
