I had some problems when I first started playing PT and perhaps the same thing happened to you.

In my case, I wanted to use the pollen from one plant to pollinate all the others to see what I got (I was making a breeding chart and was crossbreeding every plant with every other plant).

I did not realize the game moves the 'selected plant circle' to the donor plant when pollinating. So, after breeding the donor plant's pollen with the first plant, the pollen that I was using for the second pollination was not the original donor pollen, but the pollen from the first pollinated plant.

If you have extra seeds left over from that crossbreeding, check their parental lineage on the seed tray page to see what you actually crossedbred and let us know .