Flow currently has no ability to do true Filter Logic. You can allow for OR in Decision elements, but even then, this does not allow the true (1 OR 3) AND 2 sort of logic that we have access to in Salesforce.
This isn't even the biggest problem, however. With the release of sObject Variables and Collections, we have no way of doing any OR logic in that collection process. There is also a gap for Dynamic Choice generation as well, when we may one to collect all of the choices that allow for OR logic.
Example screenshots of what this would look like: