Vector v1 is corrupted. It contains "NaN" at the most of its values. Matlab subtracts only at positions where v1 contains valid numbers.
Run the following script, to see what I mean:
close all;
clear all
% Load v1 and v2
load('TwoStrangeVectors.mat')
%define an area of interest
t=2000:2030;
% Plot vector 1
subplot(3,1,1)
plot(t,v1(t),'-ro'); zoom on; grid on;
title('a piece of vector #1') % xlim([1 10000])
% Plot vector 2
subplot(3,1,2)
plot(t,v2(t),'-b*'); zoom on; grid on;
title('a piece of vector #2') %xlim([1 10000])
% Plot vector 1 minus vector 2
subplot(3,1,3)
plot(t, v1(t)-v2(t), '-ms'); zoom on; grid on;
title(' a piece of vector #1 - vector #2')
