additionally, there should be special tiles with both trees available in some tilesheets - I know those exist for VXA, and that is what you state to use on your profile even if you posted in VX (which is a different engine than VXA)
You should be able to fix this by editing your tileset in GIMP/SAI/PS or any other image editor that lets you save an image with a transparent background. What you want to do is called "clumping", it's where you move your assets around and overlap them to make them look more natural.
Ack, I've got to make a script support thread... I hate doing it now; I feel like an annoyance to people. Especially because my questions are usually stupid. Or, at least I assume they are when I don't get any replies lol. Oh well, I'll just make it in the morning. No point doing it now if I'll be asleep.