It means not to worry about things that have already happened. Just like the milk can't be put back into the glass, you can't change what has already happened. This is a pretty common phrase and a nice one to use when someone if upset about something in the past.

it means, don't be upset/angry/sad over something that has already happened and cannot be reversed/changed.

Don't get upset over something that has already happened and is really unimportant.