In[1]:=x0=0;x3=5;
F[x_,y_]:=0.25`(4044.44444444445`-66.66666666666667`x+E^(-0.015x+0.015y)(-4044.44444444445`+66.66666666666667`y))^2;
H[x_,y_]:=Integrate[0.25`(E^(-0.015`t)(E^(0.015`t)(4044.44444444445`-66.66666666666667`t)+E^(0.015`y)(-4044.44444444445`+66.66666666666667`y)))^2,{t,x,y}];
NMinimize[{27+3*(F[x0,x1]+F[x1,x2]+F[x2,x3])+0.2*(H[x0,x1]+H[x1,x2]+H[x2,x3]),x0≤x1&&x1≤x2&&x2≤x3},{x1,x2}]
Out[4]={4.457054464608864`*10^8, {x1 -> 0.06690213249753463`, x2 -> 1.1629357790698616`}}
If I did not make an error typing this all back in again then I cannot explain what your problem is. But I believe you have larger problems than this. Quit kernel and restart
In[1]:=a=1/4;b=4044+4/9;c=66+2/3;d=15/1000;x0=0;x3=5;
F[x_,y_]:=a*(b-c*x+E^(-d*x+d*y)*(-b+c*y))^2;
H[x_,y_]:=Integrate[a*(E^(-d*t)*(E^(d*t)*(b-c*t)+ E^(a*y)*(-b+c*y)))^2,{t,x,y}];
NMinimize[{27+3*(F[x0,x1]+F[x1,x2]+F[x2,x3])+ 1/5*(H[x0,x1]+H[x1,x2]+H[x2,x3]),x0≤x1&&x1≤x2&&x2≤x3},{x1,x2}]
Out[4]={7.388367735069655`*10^6, {x1 -> 2.4650125379662637`, x2 -> 3.9306108222644514`}}
So very tiny changes in your coefficients give very different results.
I would suggest you spend a few days reading about the details of approximate and exact and machine precision mathematics as provided by Mathematica. Much of that is probably not what you would expect it to be.