
Are you certain this is in her urine and not coming from her vulva. I had just one bitch who after being mated, twice, came back into a quite coloured discharge through her final week at which point I thought she's never 'taken'. This was completely unlike any of my other bitches had done after being mated. However, as she was otherwise fine, I left it and she had an uneventful pregnancy and 9 super puppies - probably the best litter we'd ever bred.
I think you should probably collect some of her urine and have your vet test it.