Regan, I recommend that you take it back to the shop - they have a responsibility to point out flaws to you like this.
I agree with the others that it is likely foxing, and caused by changes of temperature and the fabric not being able to dry out properly. It's common on older garments sadly - because it's cotton you may be able to get it out by soaking in an oxy cleaner but there is a risk the colour will run or you'll damage it in some way. If you can reach a happy solution with the seller it will help. A garment with foxing should be very inexpensive, especially if the stains won't come out (which is always a possibility).
It irks me when sellers sell items that have flaws: I certainly expect better from a vintage shop, but due to the darkness it's possible they didn't realise so if you give them the chance to make it right, hopefully they will.