As explained in Meta.SE question Where is very low quality Flag, the VLQ flag can be missing from available flags if the question is already undergoing triage, and this is by design.

While it makes perfect sense that the flag is not available while reviewing, it was very puzzling to me why this happens when I reach the question in the usual way. I had to search the Meta for explanations.

The first question mentioned has a great comment:

Might be a good idea, then, to put something in the UI to indicate this? Grey out the option with an explanation, maybe. After all, close votes aren't even visible at all below a certain rep level, so there's no way for a low-rep user to actually know why the VLQ flag is/isn't present on a given question, which seems like it'd be a bit confusing. – Billy Mailman Feb 26 '15 at 18:19

The purpose of this is basically to promote this comment to an actual feature request:

In case the VLQ flag is not available due to ongoing review, show an inactive option in the list with an explanation of why it is not available instead of just hiding it.

This is intended to reduce user confusion.

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