Can anyone explain the phrase “쓰여져 있다”? I understand what it means but what is the root verb and how it is being conjugated?

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The root verb is 쓰다(to write, to use) and the phrase is:
쓰(root)+이(passive suffix)+어지(passive auxiliary verb)+어 있다(auxiliary verb that indicates a state remains)

but it should be ‘쓰여 있다’ or ‘써져 있다’ in Standard Korean.

There are several ways to change an active verb to passive verb in Korean, and these are two of them:

1. use a suffix 이/히/리/기
쓰다 (to write) -> 쓰이다 (to be written)

2. use an auxiliary verb (어/아)지다
쓰다 (to write) -> 써지다 (to be written)

It is a common mistake to use more than one of them at the same time like what you wrote: 쓰여져 = 쓰+이 (passive suffix)+어지(passive auxiliary verb)+어.