Is your flow scheme the anaerobic upflow reactor followed by extended aeration?

There are some things you can look at in anaerobic processes microscopically, but few in the world know how to do this. Most commonly, if there's insufficent COD removal with anaerobic it's because the reactor is stuck. Check the pH and the volatile acid to alkalinity ratio here. Also what is the hydraulic and organic loading rates vs the design rates for the reactor?

As for aerobic processes and higher life forms (ciliates, rotifers etc) you can't conclude anything about sludge age here. Rotifers can grow in a sludge age of 4 days. More than anything they can indicate toxicity (lack of them) and indicate amount of dispersed bacteria- which coorelates to the amount of soluble cBOD left.

If you're seeing rotifers and cilliates in at the end of your aerobic stage I doubt there's any inhibition going on.