Stimulus control means that not only does the dog do the behavior on cue, but she doesn't do some other behavior when you give the cue, and doesn't do the behavior in question in response to a different cue.
That means, in a training situation, she does "down" ONLY when you cue down, not when you cue "sit" or "stand," and that she downs, and only downs, when you cue "down," the first time.
It's very common for a positively-trained dog who hasn't yet reached true stimulus control to "mix up" what should be "known" cues.
In traditional training, the dog is being punished for wrong answers, and so is motivated to avoid wrong answers. But additionally, the dog IS receiving information which allows her to distinguish the wrong answers. So stim control tends not to be a problem.
In positive-reinforcement training, we are relying on extinction (lack of reinforcement for wrong answers) to do that job for us, and it's a whole lot easier for incorrect responses to hang on a lot longer since the dog may be willing to keep offering the wrong response if it pays off even infrequently.
How come it pays off at all? Because we aren't really paying attention to what we are reinforcing.
If I teach "sit" first, and then teach "down," my dog is likely to offer a lot of sits during the training process. I may reinforce "sit" even if I cued "down," on the theory that the dog is getting frustrated, or because I just slipped up. Now the dog is getting reinforcement for both sit and down when cued "down." That's confusing.
Further, even if I don't reinforce the sit in response to a "down" cue, I might re-cue down. Now the dog figures out, "guess 'sit' wasn't the right choice... must be that other thing," lies down, and gets rewarded. So basically there's no real percentage in learning the right cue, because you will always end up giving her the answer.
By the way, this is one reason NEVER to add a cue until the behavior is really solid -- your dog may end up not really knowing what it means. Until you are systematic about stim control, your dog is going to be confused sometimes.
How do you fix it?
If you are teaching sit and down using luring, which I am totally OK with for most dogs, teach them separately. I would teach down first if possible, and lure it from a STAND. Then put it on cue. THEN teach sit and put it on cue. If you have already taught sit, reteach down by luring from a stand. This makes a huge difference and helps the dog understand that down is NOT "the thing you do after a sit if you don't get a cookie for sitting."
For "go to mat" and "go to crate," back up and make it very easy for her to get the cued behavior right. If you are working the mat, put the crate ten feet away and stand next to the mat. Reward a bunch of times for getting it right. If she goes to the crate, just shrug and "turn off" (like someone pulled your plug) for about 10 seconds. Then in another session, switch the positions so the crate is near you, and work the crate cue. Then in another session, put them about equidistant. Reward ONLY if she gets it right the FIRST time. If she is getting 80% or better, you can go on to more difficult choices (e.g. you're next to the mat, you send to the distant crate). If she is getting 60-80%, make the correct choice the easier one again for a while.
This should fix it.
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