
Certainly had multiple bags, and also had the horrid liquid in a bag with mummified pup, (had two in a litter born like it they were half the size and one didn't even have a cord anymore).
I assume the dark liquid was the placenta disintegrated in amniotic fluids.
With your pup I wonder if he started out as a rare twin in one bag, and was absorbed along with it's placenta, hence the colour of the liquid.