incorrect number of subscripts on matrix in R

I think that when you read in your "D1.txt", "D2.txt"................"D45.txt" files they get converted to matrices and that is why your particular for loop fails. I’ll use your example:

L <- replicate(5, expand.grid(1:10, 1:10)[sample(100, 10), ], simplify=FALSE)

If we use class(L[[1]]) to pick out the first element of the list it will output [1] "data.frame" if you use your for loop on this list that only contains data.frames you will see no error and it will give you what you want. If however we transform all elements in the list to matrices:

for(i in seq_along(L)){
     L[[i]] <- as.matrix(L[[i]])
}

and check with class(L[[1]]) it will output [1] "matrix". If you use your for loop now on L which now contains matrices we will get:

> L <- lapply(seq_along(L), function(i) { 
+   L[[i]][, paste0('DF', i)] <-  1
+     L[[i]] 
+     })
Error in `[<-`(`*tmp*`, , paste0("DF", i), value = 1) : 
  subscript out of bounds

Hence, you can either make sure that when you read in your files they are coerced to data.frames, use @Richards solution, or read in your files and coerce them to data.frames via

 for(i in seq_along(L)){
    L[[i]] <- as.data.frame(L[[i]])
}

and use your for loop.