Soba noodle cooking water?

I ate cold soba noodles at a restaurant and the waiter came in with a can with what I believe was the boiling water for the noodles.

Not sure what it was for but I drank it up.

Did I do wrong?

Yes, it is the boiling water from the soba, which contains a considerable amount of nutriens. You mix the water with the remaining dipping sauce and drink it. It is called sobayu:
https://www.google.com/search?q=sobayu

You had already got the correct answer but let me add that even some Japanese do not know it. Personally, when I was young, near Soba restaurants did not server it. So I got frozen at first time when it was served.

In my experience, not many shops do this, but it makes for a nice drink at the end.

Don't worry, what you did was correct. As Uji explained, some soba restaurants serve boiling water. Most customers drink it by mixing with the dipping sauce, while some drink it directly just like you did. (I prefer the former)
Most soba restaurants offering that service tend to be expensive ones, but recently I noticed that Fuji Soba, one of the famous cheap soba restaurant chains, also does the same.

To set the records straight, establishments that do that are the "proper" ones.

They're not necessarily expensive nor are they uncommon. A proper soba restaurant that boil non-chemical soba inhouse is always ready to give you "soba-yu" literally meaning "soba hot water". If they don't serve it automatically, you can ask for it.

And you don't have to drink all of what's in the pot. A lot of people would pour a cup or two in your soba-choko (where you poured your "soba-tsuyu" sauce in) and enjoy it like you would your after-meal tea.

Or, of course, you are free to order a cup of "shouchu" alcoholic beverage so that you could mix it with the soba-yu by yourself. You'd be free to adjust the amount of soba-yu and keep adding it.

I'm originally from Tokyo, so I can't finish a zaru, mori or seiro (which are the soup-less soba dish categories) without soba-yu.

Bon appetite!

Think I've had this pretty much every time I've had soba, tasty and comforting.
You did fine :)