You are changing the size of a in the loop with this line:
a(k) = [];
So subsequent iteration indexes that depend on the length of a will fail. Maybe save the indexes to delete in the loop, and then delete them all at once at the end. E.g., something like this:
a={'Time12:30','Time12:40','Time1:40', 'Time2:40'};
b={'12:', '1:'};
x = false(size(a)); % <-- Indexes to delete, start out nobody deleted
for k=1:numel(b)
x = x | ~cellfun(@isempty,strfind(a,b{k})); % <-- Flag the ones that b{k} matches
end
a(x) = []; % <-- Delete all the flagged lines at once
