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With a young puppy, potty training is much more likely to be about physical development than intelligence. Just like human toddlers, a puppy is still developing both their ability to actually hold their bladder and their ability to tell when they have to pee. It could be that she's just a little slower to mature (physically) than previous puppies you've had - I can't speak to whether that's a breed thing since I have no experience with potty training either shepherds or collies.

This is a case where I'd set her up in a pen. Her sleep area (can be her crate) at one end, and a potty station at the other. Ideally, this potty station would be using the same substrate that she'll be going on outside - a piece of turf, for example, or gravel, but at the very least I'd put in something like paper pellet litter, so it's not like anything else in the house. This should give her the opportunity to potty away from her sleeping area, and imprint on the substrate she'll be pottying on outside (if you go that route). You can wipe the potty area substrate with a towel you've used to mop up an accident to make it more appealing at first, or even cover it with a puppy pad that you slowly cut smaller and smaller until she's going just on the station substrate. You should still be giving regular breaks when possible outside so you can reward for pottying there, but if you need a longer-term confinement solution this would be my go-to.

Otherwise, she sounds like a puppy you'll have to set a timer for whenever she's crated, at least for now. Starting with every 30 minutes, increasing the increment length if she's doing well, and decreasing if she has a setback. It sounds like a lot because it is, but if it gets her past this stage of development where she's struggling to hold it, then it's worth it.

My eldest was also pad-trained before I got him, and I agree that it does make things harder - at least for some dogs. I may use pads as a management tool in a pinch/emergency (eg covering the puppy's pen with them if I absolutely cannot take them outside for some reason - extreme weather conditions for example) but I wouldn't praise for it or otherwise encourage a puppy to use one regularly. I feel your pain there. It's natural for dogs to prefer an absorbent surface anyway, but pad-trained dogs often seem to be particularly keen on seeking out rugs, bathmats, that shirt you dropped on the floor on the way to the laundry, etc.
 
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