Maybe values in PreLabel are getting overwritted again and again because you have not defined it to be an array. Define PreLabel to be array like PreLabel(i) so that it can store values for different folds.Similarly if you require values for other variables for every fold define them to be an array as well
for i = 1:nfold
test = (indices == i); train = ~test;
[Prior,PriorN,Cond,CondN]=KNNtr(train_data(train,:),train_target(train,:),Num,Smooth);
[HammingLoss(i),RankingLoss(i),OneError(i),Coverage(i),Average_Precision(i),Outputs(i),Pre_Labels(1)] = KNNte(train_data(train,:),train_target(train,:),train_data(test,:),train_target(test,:),Num,Prior,PriorN,Cond,CondN);
end