There was a charge for tea or the use of a private room, but I wasn’t told that in advance.

In Japan, some restaurants serve tea or water for free while others charge. If there is a charge, it should be listed on the menu, so check. For a private room, especially at dinner time, there may be a separate charge. There should be an explanation to that effect on the website or when making a reservation, so check that again, and if you don’t find any such notice, you can let the restaurant know.