This bug is hard to describe and hard to screenshot, so I'll do my best.
I had a total of 27 cauliflower. Two stacks of 10 and one stack of 7. I made all the cauliflower in the stack of 7 into seeds, and then clicked on one of the stacks of 10 to make seeds. Strangely enough, the first seed bag I made after clicking the stack of 10 came from the OTHER stack of 10 cauliflower! The second seed bag came from the stack I clicked originally. So instead of having a stack of 8 and a stack of 10, I had 2 stacks of 9. This has happened several times with several different types of crops.