Wait how did you add different colors/colours to the sprites and tiles while they mostly are the same?
To use more than 3 colours in a screen at the same time you can do something like this in the game data window. Find the palette you want to use and add a couple more RGB colours on lines underneath. For example:
NAME Black green
I have added 133,212,201 & 249,252,246 into the game data.
Then (again in the game data window) find the tile you want to change the colour of, and underneath the line that says either WAL true or WAL false add COL plus the number row of the colour you want to use - don't forget that Bitsy starts counting at 0. For example:
NAME mistletoe 1 green
COL 4 will give the mistletoe 1 green tile a colour of 249,252,246
When you click out of the game data window after editing the text the tiles will change to the correct colour. :)