Never mind, I figured it out. I had the index wrong. It should be like this:
AA <- 1:rowlength
BB <- 1:ncol(Nmatrix)
for(i in AA){
for(j in BB){
if (is.finite(TMatrix[i,j])==FALSE){
TNS <- matrix(data=NA,nrow=1,ncol=4)
TNS[1,1] <- TMatrix[i,j]
TNS[1,2] <- Nmatrix[i,j]
TNS[1,3] <- rownames(TMatrix)[i]
TNS[1,4] <- colnames(TMatrix)[j]
TMinf <- rbind(TMinf,TNS)
}
PMatrix[i,j] <- pt(TMatrix[i,j],n1+n2-2)
}
}