Why are you using eval? There is no real reason you should need it. Same goes for length: what you actually mean is numel (or perhaps size).
Anyway, the cause for this problem is that you are plotting your data twice, first with red and then with blue. You are not changing the color for each row of your data.
matrix_A = [1 2 3 4; 5 6 7 8];
matrix_B = [9 10 11 12; 13 14 15 16];
col = {'r', 'b'};
data = {matrix_A, matrix_B};
x = [20 30 40 50];
figure
fig = tiledlayout(1,2);
for i = 1:numel(data)
t1 = nexttile(fig);
for data_row = 1:size(data{i},1)
plot(t1, x, data{i}(data_row,:), 'color', col{data_row});
hold(t1,'on')
end
end
