Data Values do not plot in correct position using scatter() when xlim(), ylim(), or panning of the figure is performed.

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I've been having an issue trying to adjust the limits of my figures after plotting using the scatter() function. Here's the code I use to plot.
scatplot = scatter(scatterX, scatterY ,200, plotmarker, 'DisplayName', string(topdirList(ijk+2).name));
scatterX and scatterY are both vectors. I use this function in a for loop, and can post the for loop if it may be the problem. When I plot, I want to adjust the y-axis so that the figure looks better. The first image is of the figure without any limits changes or panning.
The next 2 files are images of the figure when I begin panning upward.
As you can see, panning changes the y axis values. The highest value red X is 100 in the first image, and changes to 97.5 in the third image. 100 is the correct value.
I have no idea what is going on. How can I get the axis to stay correct in values when panning and changing limits?
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