If there are less items in Speed then Time, then your if statement should use length(Speed) instead. However, that may not always be the case. Perhaps use the min length from either?
for i = 1:min(length(Time),length(Speed)) %Create a loop that continues up until the last value of time in the column
ChangeinTime = Time(i+1)- Time(i); % Calculates the time difference
ChangeinSpeed = Speed(i+1)-Speed(i); % Calculates the speed difference
Acceleration = ChangeinSpeed/ChangeinTime; %Calculates Acceleration
dataAccel = [dataAccel;Acceleration]; %Stores acceleration in empty array
end