Given the DA I smell a rat too – but your E/C did agree to the removal of the tree/s albeit unintentionally, so you can hardly blame your Strata Manager.
What can you do? Not much after the event, but in most circumstances the Local Council should have been approached for its consent to the removal of the mature trees under its Tree Preservation Order.
You could contact the Council to ascertain if a consent was granted, but be cautious as if none was granted the Council could look to prosecute, and the easiest “mark” is probably the Owners Corporation as property owner.
Sorry I can’t be more supportive of your situation, but I do understand your concerns and would feel the same way in the circumstances.