I am not sure what graph you want to get but the following code does not throw an error. Notice that I put back ticks, `, not single quotes, around Percentage or Time (%) and I moved the stat and position arguments inside of geom_bar.
ggplot(ThreeSpecies, aes(Species, `Percentage of Time (%)` , fill=Stage)) +
geom_bar(stat="identity", position = position_stack(vjust = 1)) +
theme(panel.grid.major = element_blank(),panel.grid.minor = element_blank()) +
scale_y_continuous(labels = scales::percent_format(scale = 100))+
ylab("Percentage of time to blastocyst(%)")+
xlab("Species")+ guides(fill=guide_legend("Stage"))