"1) Wrestler A is on top starting in referee's position. On the whistle, B immediately stands up and suddenly they're both out of bounds...."
When you couldn't tell whether B was running out of bounds or A was pushing out of bounds, no call is the right call. Warning both wrestlers after each OOB scenario is also appropriate and helpful. But at some point you have to figure out who is causing OOB and penalize one, or both, wrestlers.
A couple of tips: If the offensive wrestler is bent at the waste and his shoulder is in the back of the defensive wrestler, there is a very good chance that the offensive wrestler is driving the situation out of bounds. Look at the offensive wrestler's shoulders to see if he is trying to return the wrestler to the mat, or just following the other wrestler, or actually trying to drive the defensive wrestler OOB.
Another item to look for is foot prints on the edge of the mat. You only have a second or so to see them, but if you look at the footprints the two wrestlers left in the mat just before the OOB line, and you see one set of toe prints (pushing out of bounds) and another set of heal prints (digging in to stay in bounds), you'll know how to call the situation. But you have to look fast because the mat indentations disappear quickly.
One more thing on this scenario - if you believe that you saw the defensive wrestler run for the edge, and then stop and dig in, and the offensive wrestler then push the defensive wrestler out, the right call could be stalling on defense (playing the edge of the mat) and TV on offense (forcing your opponent off the mat). That's sure to tick both coaches off, but it can also drive home your warnings to the wrestlers that all wrestling should happen in the middle.
"2) Wrestler A is on top and ahead by 1. Wrestler B keeps getting broken down, then getting back up to his base, then broken down, then back up to his base..."
This is a tough scenario. You can't penalize wrestlers for just being bad at the craft (though we may like to ), and it could be that what you were witnessing was just extra-ordinarily bad Jr High wrestling. But if you were to decide that either wrestler is stalling, you (and the wrestlers) will be better off if you make that decision early in the match. That way you set expectations for the wrestlers and coaches, and you give the wrestlers a chance to wrestle correctly (aggressively) before the final seconds.
If you were to let this situation stand until the last 20 seconds and then call stalling, you've become a factor in the match on two counts. First with the 1:40 of non-calls, and then with the stall call in the last 20 seconds.
All I can suggest here is make up your mind early, and then act (or not) consistently through the rest of the match.