The same is true of pretty much any urban / suburban rail network where ever you look.
Peak times are by definition busier - there are more trains and more passengers and when you combine that mix there is more potential for delay no matter how well run the railway is.
The fact that Metro is meeting its targets suggests that the network as a whole is being run reasonably well. Connex seemed to be rather poorer at achieving less demanding targets with fewer trains for example.
When there is the unpredictable and sometimes erratic behaviour of the Great Australian Public to factor in it might be a surprise to some that Metro manages as well as it does. Every time a school-kid holds a door open for their mates, every time a train develops a fault (which requires contact with Metrol whether or not the train is still able to run), every time wild weather interrupts the service, even a train which happens, quite reasonably, to collect multiple wheelchair users along its journey - all of these are beyond Metro's control but affect performance.
Metro has been accused of "cheating" and skipping stops to meet its target. Yes stops are skipped on some occasions but almost always when there is another train within a few minutes of the late runner which is trying to regain time. The alternative is to serve all stops, collect possibly a double loading of passengers which takes more time and become even later. Ultimately the train is then so late that a trip has to be lost altogether.
"Bashing" the local rail operator is virtually a world-wide sport. Metro does better than many at its task.