since when did a flag become a symbol meaning to report something?

It just means to mark something for review. In other places flag is a good thing. Here is the word origin.

flag (v.2)

1875, "place a flag on or over," from flag (n.1). Meaning "designate as someone who will not be served more liquor," by 1980s, probably from use of flags to signal trains, etc., to halt, which led to a verb meaning "inform by means of signal flags" (1856, American English). Meaning "to mark so as to be easily found" is from 1934 (originally by means of paper tabs on files). Related: Flagged; flagging.

Flagging some thing has meant taking note of it for quite a while.

It Always has been that way on Yahoo Answers Since Day 1

Back in ww2, a mine sweeper woyld walk ahead of a convoy with a metal detector and mark a spot with a mine using a flag, usually brightly coloured, to warn the convoy to avoid the spot, and for the attention of the disarm and dispose team. Same basic idea, flagging a post as something requiring technical attention to make it safe

Here, the report icon is a flag. In the business world things get "flagged" for follow up, which means someone may make a note or stick a bookmark (flag) at a spot in the text, for attention later.

To flag something is to mark it for further review, which is what happened to reported posts here at one time. The flagged posts were reviewed to see if removal was appropriate or not. That ended when we lost our YA Team. Now they are only reviewed if appealed.