I don't believe it happened. At least it did not happen in The Roundheads. There Ben got separated and alone of all the TARDIS crew found himself in Amsterdam.
Please, correct me if there was another Second Doctor visit in another story. Amorkuz☎ 22:46, June 18, 2016 (UTC)
As there is no mention of Amsterdam on the Second Doctor page, I've removed the category from Amsterdam for now. If we find out later that he did visit the city, it can be re-added. Shambala108☎ 23:11, June 18, 2016 (UTC)