First:
doc interp1
and once you understand roughly what it does and its input parameters, I guess that you could modify your code a little bit as follows (untested):
lambdaMJ = 7.2;
MJ_Flow = (30/60)*2;
A = 100;
B = 1;
C = 70;
D = 4;
E = C + D;
F = A - C - D;
MJ_start=0;
% NEW
n = 100 ;
step = 0.5 ;
tGrid = (0:step:F).' ;
lambdaMJ_sec = zeros(1, n) ;
Major_end = zeros(1, n) ;
Major1 = zeros(length(tGrid), n) ;
for a = 1:n % Updated: upper bound.
Num_cylces = 1;
XMJ=(poissrnd(lambdaMJ, A, Num_cylces));
lambdaMJ_sec(a) = mean(XMJ)/10;
%
FMJ_cars_wait = @(T11,MJ_V11) (lambdaMJ_sec(a));
[T11,MJ_V11] = ode45(FMJ_cars_wait,[0,F],MJ_start);
R_G_MJ = MJ_V11(end:end);
%
FMJ_cars_wait_2 = @(T12,MJ_V12) (lambdaMJ_sec(a) - MJ_Flow);
[T12,MJ_V12] = ode45(FMJ_cars_wait_2,[F,A],R_G_MJ);
%
Major_end(a)=MJ_V12(end);
MJ_start=MJ_V12(end);
if MJ_start < 0
MJ_start=0;
end % Updated: no else clause.
%
Major1(:,a) = interp1(T11, MJ_V11, tGrid); % Updated: interpolate.
end
