The my simple case:
Plotting graphs within the loop brings different results than plotting it directly after the loop
# Initialize
Input <- list(c(3,3,3,3),c(1,1,1,1))
  y <- c()
  x <- c()
  plotlist <- c()
  Answer <- c()
  # create helper grid
  x.grid = c(1:4)
  y.grid = c(1:4)
  helpergrid <- expand.grid(xgrid=x.grid, ygrid=y.grid )
  #- Loop Lists -
  for (m in c(1,2))
  { 
    # # Loop within each list
    # for(j in 1:4)
    # {
    #   y[j] <- Input[[m]][j]
    #   x[j] <- j
    # }
    y[1] <- Input[[m]][1]
    x[1] <- 1
    y[2] <- Input[[m]][2]
    x[2] <- 2
    y[3] <- Input[[m]][3]
    x[3] <- 3
    y[4] <- Input[[m]][4]
    x[4] <- 4
    Points <- data.frame(x, y)
 # Example Plot
    plot = ggplot() + labs(title = paste("Loop m = ",m)) + labs(subtitle = paste("y-values = ",Points$y)) + geom_tile(data = helpergrid, aes(x=xgrid, y=ygrid, fill=1), colour="grey20") + geom_point(data = Points, aes(x=Points$x, y=Points$y), stroke=3, size=5, shape=1, color="white") + theme_minimal()
    # Plot to plotlist
    plotlist[[m]] <- plot
    # --- Plot plotlist within loop ---
    plot(plotlist[[m]])
   }
  # --- Plot plotlist outside of loop ---
 plot(plotlist[[1]])
 plot(plotlist[[2]])
Here is an image of the results: Plot Results
as aaumai is pointing out that there is a nested loop that might cause the issue for ggplot using static values, however the resulting plot 'is' showing the correct y-value (y=3) explicitely, but the geom_points are using the wrong values (y=1)...
It makes absolutely (!) no sense to me, I am relatively new to R and trying to debug this for hours now - so I hope someone can help me with this !!
EDIT: I manually removed the nested loop and updated the example code, but the problem still persists :(
 
     
    