We can only guess since you're not sharing your code. My guess is that you made the all too common beginner mistake of thinking (x,y) is (row, column). It is NOT. (x,y) is (column, row) and (row, column) is (y, x). Make sure you know which you are using.
The other option is that you were plotting in a different/new axes where the y axis is flipped. Remember, for images, y is 1 at the top and increases going down and for plots, y increases going upwards.
