You have two problems.
First off, the syntax for that first INNER JOIN is not correct. You are conflating the INNER JOIN and ON parts of the statement. (At least, I think this is the case, unless you actually have "." characters in your table names are really want a cartesian result from this JOIN)>
Secondly, the second usage of EntityID (in that new INNER JOIN you added) could refer to the EntityID value from either the left or right side of the INNER JOIN -- that's what the "ambiguous column" in the error means.
Here is some SQL to get you started. It follows the selection logic you give in the comment, below. It names each table with an alias and ensures that each column specifies the table from which it should be drawn. I don't have an instance of MySQL handy to try it, but it should get you started.
SELECT E.EntityID, SUM(EED.Frequency)
FROM entity_epoch_data EED INNER JOIN entity_dataitem_relation EDR
ON EED.EntityID = EDR.EntityID WHERE EDR.entity_dataitemtype = 3
RIGHT OUTER JOIN entity E ON E.EntityID = EED.EntityID
GROUP BY E.EntityID