The Flatten layer support sequence input only. [1]
As i understand from your network architechture you don't need Flatten Layer. in Matlab Flattenlayer is for merging height,width and channel of input in an aray for N data in minibatch and S (number of sequences) series data. the output is a 3-dimensianal array with size of (H*W*C)xNxS.
if you use a fullyconnectedlayer(fc) as you did after Flatten layer, the input array of fc layer which is comming from a Conv layer become vectorize in a spatial domain in output of layer.
so just deleting the Flatten layer will solve the problem.
