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.
If only RM had the capability to show whether a project has been edited, or not... like 99% of all other editors out there. That don't cost, too, or release new versions with very few features just to get the extra money... ugh, just too many basic features missing even after, what, two decades?