When you use "my_ANN = train (net_set, input,output)", your network will have a input/output size of 49736, which results in many weights in your network. If you use "my_ANN = train (net_set, input.',output.')", the network input/output size is only 3 and the weights in different layers are small so you can train the networkd with no problem.
net_set = fitnet (4, 'trainlm');
output = randn(49736, 3);
my_ANN = train (net_set, input',output');