Which sentence is correct?
- Why has my order not shipped out?
- Why is my order not shipped out?
Can someone tell me the grammatical rule on this? When do I use “has” and when do I use “is”?
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Neither one is really correct because you're asking whether someone else has done something with your order, which uses a passive construction. The idiomatic way to ask is
Why has my order not been shipped out?
This is because, in statement form, the company has shipped your order, so your order has been shipped by the company.
(To make things more confusing, people do sometimes say "The order shipped yesterday", using an active construction, but this is a rather slangy, informal usage.)
To answer your larger question about is vs. has:
We use is with adjectives, and with participles in the present continuous tense or passive constructions in the present. Basically, use is if we're talking about something happening right now.
We use has with participles in the present perfect. Basically, use has if we're talking about something in the past that remains true.
(Note that these are not the only things you could use - you could also say "my friend had been eaten by a bear" or "my friend was eaten by a bear" - but you asked specifically about is vs. has.)