
If you buy a non reg. pup from non reg parents, theres a pretty high chance that either the parents are a long way from the breed standard, or are to some degree crossbred.
So she could be x bred even if both parents you saw are her actual parents, or.. it may be that another dog got to her mum when she was in season. I have noticed a lot of folk dont realise a bitch can carry pups by several different fathers at the same time. You will just have to wait and see as she grows up.
The colours do not sound 'wrong', though I am not up on SBT colour genetics, red pups from a fawn (i assume related to red genetically) and black (can hide red) parents doesnt sound 'wrong'. SBTs can be pretty much any colour and these are non reg so could be crossbreeds which gives even more potential colours.
The weeing issue is likely due to how the pups were raised - if they have always toileted on soft beddingy type material then that is what will seem 'right' to them - the only way to fix this is to be super vigilant and take the puppy outside very very frequently so she has very little opportunity to go on soft material. Then you reward her for going outside so you both change the habit from soft bedding to grass, and reinforce that with the rewards.
In effect this means taking puppy out every hour, and after food, sleep, play, drinks, and when she looks like shes seeking ou a place to go.
Do not punish her for an accident, any accident is your fault, not hers. Punishing for accidents just leads to a pup who avoids going in front of you!