"One of those is flags"

Those is plural, yes, but "is" grammatically agrees with one in this case.

The sentence is something like this:

Stack Overflow, due to its size, has some unique problems. One {of those [problems]} is flags.

The part between [-] can be omitted to avoid repetition. The part between {-} can be omitted to explain the agreement.

So it could become: "One is flags".

EDIT: I'd like to add that the sentence "One of those is flags" written by Jeff, is perfectly fine. It's not nonstandard or ungrammatical. It's correct in English.

Like I said in the comments, "flags" is treated as a general noun, not as a plural of many objects. It's like saying "One of those is the flagging system".

Let me highlight the sentence as :

One (of those problems) is flags

The "is" agrees with the "One" in this case.

I think that the main reason this sounds wrong is that the word ”flags” is used actually to refer to ”flagging system” or ”flagging concept”, singular. If such substitution is made, there are no problems with the original.

Alternatively, rewriting it like

One of those is related to flags.

seems (to me) more grammatical compared to the original (meaning is changed though; maybe caused by is closer to original intention).

EDIT: After opening a new question regarding this subject I should correct myself - there is nothing ungrammatical in the original line and the improvement I propose is just the matter of style.

Note that flags is not exactly plural but it is a feature (not mutiple features , not a plural.)

  one is typo

  One is 'flags'  

  One {Among these} is 'flags'

  One {of these} is 'flags'

That is how it happens!