What exactly are the problems you are having?
I can't imagine excel is acutually putting the dots in the wrong spots and you say you are using a scatter plot.
Just guessing, but I imagine you have some data with a lot of scatter(unknown,y) and a small range(known,x) and are trying to fit a line to it, and excel is giving you a line that you find wrong. Its probably that you don't have enough data points. Either get data points farther out from your range (you'll need less data points) or get more data points in the same range (will need many more data points).
Lets say you were plotting dice roll out comes.
You have die 1, 2, and 100.
Lets say you roll die 1 and 2 each 2 times.
die 1 gives you 6 and 5 with die 2 giving you 1 and 3
from this die 3 should have a roll averaging -1.5
of course we know the trendline should be horizontal at 3.5
To get a much more accurate graph only one or two rolls with the 100 die would give almost a horizontal line, or you are going to have to roll die 1 and 2 enough times that they both give an accurate median of their values (Not going to do the stats, but I could imagine needing 10 or more rolls per point)