Blakey
It sounds as if you did have some meniscal damage with the initial injury, which is usually the case with an ACL tear. Not allmeniscus tears are visible on
MRI. Just like an X-Ray, an MRI is a still picture and doesn't show what the structures of the knee do when moving.
During surgery the surgeon can move the knee and also detect a meniscus tear better.
Anyway, if they did take out something, it was probably a meniscal body.
I would say that if your range of motion (both flexion and extension) and weight bearing is coming along, and you dont have a "locking" of the knee, you shouldnt worry about the click too much- it is only 2 weeks post-op.
Your physio will give you certain exercises, and as your muscle control of the knee gets better, hopefully that click should improve too!
If it locks and clunks, then discuss this with your surgeon at the next follow-up.
Good luck.