Your syntax is not correct. In MATLAB [] is not a list operator, it is a concatenation operator. So your code does not form a "list": it simply concatenates all of those cell arrays into one single cell array. You can check this out yourself:
>> a = [{1,98,99} {1,2,6} {4,5,6} {7,8,9} {3,45,78}];
>> class(a)
ans = cell
>> size(a)
ans =
1 15
To perform your task you should create a cell array of numeric arrays, like this:
>> a = {[1,98,99],[1,2,6],[4,5,6],[7,8,9],[3,45,78]};
>> xx = [1,2,3];
>> idx = cellfun(@(v)any(ismember(v,xx)),a)
idx =
1 1 0 0 1
The vector idx gives the logical indices: logical indices are often faster and simpler to use than any other indices, but if you really need the subscript indices then use find:
>> find(idx)
ans =
1 2 5
