Learn Hardcore Russian: Не наливай кипяток в кружку сразу, подожди минуту. - Don’t pour boiling water into the mug right away; wait a minute.

With negative commands in Russian, the imperfective imperative is very common/preferred: не наливай = don’t be pouring / don’t pour (in general / at this moment).
Не налей (perfective) exists, but it often sounds more like don’t end up pouring / don’t accidentally pour, or it can feel more abrupt/marked depending on context. For everyday advice like this, не наливай is the natural choice.

What’s the difference between наливай and налей without не?

Наливай! (imperfective) can mean pour (some), keep pouring, go ahead and pour—it’s less focused on a single completed result and can sound more “process” or “casual/inviting.”
Налей! (perfective) means pour (and finish that action)—a single, completed pour is emphasized.

Why is it в кружку (accusative) and not в кружке?

Because в + accusative is used with motion/transfer into somewhere:

наливать в кружку = to pour into a mug (direction/result)
If you describe location (no motion), you use в + prepositional:
в кружке = in the mug (already there)