Your while loop actually only runs once because after the first iteration, B>360 returns a logical array of [0 0 0 1 1 1], so it does not loop a second time. I think you meant to do something like this:
B = [361;362;363;1000;10000;100000];
for i = 1:numel(B)
while B(i) > 360
B(i) = B(i) - 360;
end
end
which will return:
1
2
3
280
280
280
