"Can you help me what is the cause for this behaviour?"
Because that is the indexing that you used.
You defined the loop iterator to go from 112800 to 152800, and you used those values as indices into y5s_unfiltered, so the last index of y5s_unfiltered that you allocate to will be 152800. MATLAB will simply expand that vector to suit those indices, which won't be very efficient.
The solution is to loop like this:
V = startSample:stopSample;
N = numel(V);
y5s_unfiltered = zeros(N,1);
for k = 1:N
y5s_unfiltered(k,1) = y(V(k),1);
Or use MATLAB's basic indexing abilities and avoid the loop entirely:
y5s_unfiltered = y(startSample:stopSample);