For anyone who might need help on this in the future, the linear layer as mentioned in the post works correctly. Using MSE loss on such data, works normally while using a cross entrophy loss, there might be an issue.
On a time step x feats data, I did not find a way to state the dim to apply softmax on. Instead you can specify it in log softmax and then use nllloss. (you get the  same loss overall with proper softmax norm)