If I'm practicing say, alternate picking with just my right hand for speed and wrist rotation am I better off just stopping and going on to something else if I'm just not dialed in that day. And for the days that I am on, go for longer than prescribed.To avoid bad muscle memory and reinforce good.
Yes, I would recommend that course of action. Your brain and muscles don't really care whether you're doing it "right", they're just going to burn it in exactly as you're doing it. So if you are not doing well it would be best to slow down, try something easier, or take a break.
You can certainly do extra while you are in the zone as well, but take care not to strain yourself or to go to the point that you've become sloppy again via tiredness or boredom.
You definitely don't want to ingrain bad technique. On the other hand, I wouldn't want you to think that you have no control over your technique. So I would recommend that when you are not able to hit your target tempo, that you practice the passage, but at a tempo that does work, while making sure that you don't have any technical problems, such as tension that might interfere with energy flow.
There are two types of muscle memory: physiological and neurological. If you're not "on" that day, it may be beneficial to determine which aspect is off because you may be able to do a different exercise in a similar vein to still get the workout that you need without reinforcing the bad habits.
If your mind is wandering, a good reset is to do a chromatic scale at a moderate tempo up to the 12th fret and then back down. You don't have to think to hard about it and you can focus mentally on the task at hand.
If your hand is failing, try dialing your metronome back a little and see if you can manage the workout at a lower speed.