A new feature in APEX 4.0 is that you can define per series what you want the series type (Bar, Line or Marker).
Lets start with an example.
We create a 3D Column chart based on the salary of the employees.
Our first Series looks like this (the Series Type is per default Bar):
select null as link, ename, sal
from emp
select null as link, ename, sal, nvl(comm,0) as comm
from emp
Now we want to add a line with the average of the salary, so we add another series with as sql query:
Make sure you select Line as Series Type for Series 2 (the average salary)

When you run the chart you expect to see the same chart as above but with a line that represents the average of the salary...
What happened is that the first value, salary, is still a bar, but the second value, commission, changed from bar to line and the third value, average salary, became a bar (that is because our main chart type is a 3D Column chart, so it takes whatever is default). So APEX doesn't take the Series type into account correctly.
The workarounds is to not use the single query with multiple values, but a single query per series.

Running the chart again shows us what we expected
(Found in APEX 4.0.2.00.07)