This is just my personal opinion on the cleaning it up thing, as I've heard about the "never clean it in front of your dog" rule too. I personally don't think that a dog can reason like that and make a connection that you cleaning it up means he can go anywhere he wants and you will clean it up again (especially a young puppy). That would mean that they are seeing something happen once and making an assumption about it happening again in the future. While I feel dogs' minds are much more complex than many realize, I don't think they make these kinds of deductions. I think it's all really just a matter of forming the right habits and routines.
I do think that they might be able to pick up on emotions when you are cleaning it though. If you are annoyed (even if at yourself for not catching it) or if you are disgusted, I think the pup can pick up on this and there can be some confusion. So I certainly don't think it hurts to have the pup somewhere else when you clean it, but I also don't think that if he sees you cleaning it he will reason out that he can just go again.
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