You need select a specific values of color for make better the plot.
For bettey hepl you, is necesary put some example about her data. dput()
Toy data
library (ggplot2)
Tratamiento = factor(c(1,2,1,2,1,2),labels=c("Testigo", "Tratado"))
Color = factor(c(1,1,2,2,3,3),labels=c("Verde","Envero","Negra"))
Aceitunas = c(72,33,11,8,17,59)
df=data.frame(Tratamiento,Color,Aceitunas)
df
ggplot(data=df, aes(x=Tratamiento, y=Aceitunas, fill=Color)) +
geom_bar(stat="identity") +
scale_fill_manual(values=c("#805115", "#FFE9AA","#8F305B"))
wiht scale_fill_manual() you could select the value of color. But you must select the same number of colors according to your fill variable.
In this link you can select the color tha you like
Pallet for select color