In Preferences>Scala>Formatter, there is the ability to set whether the formatter indents with spaces rather than tabs, and how many spaces it should use. This only affects the formatter, however, not what happens when you hit the tab key. This is controlled by Prefences>Java>Editor>Typing.

Not only is this confusing, but it also means that there's no way to have different settings for Scala and Java, which is a big problem for people like me who want to use 2 spaces for Scala code, but have a large body of existing Java code that uses 4 spaces.