I have a training set that looks like
Name Day Area X Y Month Night ATTACK Monday LA -122.41 37.78 8 0 VEHI
Even though in the help file of train said either maxtrix or data frame would be expected, but you can try to convert the matrix to a data frame:
train
model <- train(y=ynn, x=as.data.frame(mnn), method='nnet',linout=TRUE, trace = FALSE, trControl = nnTrControl,metric="logLoss", tuneGrid=nnGrid)