One simple angle is Ioannidis simply makes up some parameters to show things could be bad. Later empirical work measuring those parameters found Ioannidis off by orders of magnitude.
One example https://arxiv.org/abs/1301.3718
There’s ample other published papers showing other holes in the claims.
https://scholar.google.com/scholar?cites=1568101778041879927...
Google scholar papers citing this