The relevant file is lib/sudoku-game.vala

I think you're looking at bug #731139, which has already been fixed. Are you sure you're looking at the latest version of the code?

Sorry, the issue is actually somewhat different from what I told, but it still exists: the code does use ngettext so that's not an issue; however it still appends %d and the translation of "minute"/"minutes" which is wrong.

Do:
ngettext("%d minute", "%d minutes", minutes);

Don't do:
var minute_string = ngettext ("minute", "minutes", minutes);
var time_string = "%d %s".printf (minutes, minute_string);

Also I'm not sure the way you then insert that string in another string is that good an idea.

I'd avoid:
var time_str = SudokuGame.seconds_to_minutes_string (time);
new MessageDialog (…, _("Well done, you completed the puzzle in %s"), time_str);

Instead I'd rather have seconds_to_minutes_string directly return the full string. So you'd have something like:
ngettext("Well done, you completed the puzzle in %d minute", "Well done, you completed the puzzle in %d minutes", minutes);

Created attachment 284472 [details] [review]
Make a string easier to translate

Also, remove this logic from SudokuGame.vala, since it makes absolutely
no sense to have it there.

Hope this doesn't break anything....

Created attachment 284473 [details] [review]
Better translator comment.

Created attachment 284474 [details] [review]
Actually use a better translator comment

Apparently committing things is hard for me today.

Thanks, that would indeed solve the issue!