The alignment problems are due, in part, to your bars not representing the data you intend. The following lines up correctly:
ggplot(my_data, aes(x=day, weight=mid, ymin=mid-sigma, ymax=mid+sigma, fill=group)) +
geom_bar (position=position_dodge(), aes(y=mid), stat="identity") +
geom_errorbar (position=position_dodge(width=0.9), colour="black") +
geom_point (position=position_dodge(width=0.9), aes(y=mid, colour=group))