Try going to "league settings>stats & ai"
Top left of that screen is a setting for "Tracked statistics detail".
Set that to "very high detail" and I think the data needed for the spray chart will be saved. This setting is available for each league individually allowing a mix of detail between them and, more control over the size of your save file.
I believe low minor leagues, or maybe all, minor leagues are not set to a high enough detail to produce spray charts. So, in your case, being at rookie A ball you are not saving the data to make the spray charts.
There is also a "high detail" though I'm not sure if that would include data needed for spray charts. I do know the only league in my game that has spray charts is MLB and it is the only league on "very high detail". My minors, all set on "normal", and do not have charts. I think, though it's been a long time, that I set all of them to "normal" but have no idea what the default is anymore.
I tried searching the manual for a description of what is saved for each setting but... no matter where I looked I could not find it.
I know it used to be in there somewhere.
Hope that helps.