You'd think at least one person seeing the flag/warning would at least have the intelligence to load up the site, check what it is, then check the card account's history for similar purchases and then make an informed decision whether it's likely to be fraud or not.
Or would that be tooooo easy for us?

Not too easy, but more likely too much actual work. Working is soooo 2009, you know...

It's much more likely a script doing that work without the ability to make intelligent decisions.

It isn't always the site as the bad guys will often test newly required credit card details with a low value transaction before going for something with a bit more value. When the credit card company sees these transaction it sometimes flags them up.

Yes. Flagged to be checked by a person. Which should mean noticing if similar purchases have been made in the past year or two. THEN making a reasoned, informed decision. Or at least contacting your bank to get them to ask you if it's valid, or if your card's been stolen.
But no, it's much more easy for the slackers to just freeze your account without looking. Causing distress and anger.

Chances are it isn't GOG itself causing a flagged transaction, but whatever 3rd party is running financial transactions for GOG.

I have bought 44 games so far using credit card, i havent had any problems what so ever.