The mass transfer resistance of a sterile plug is mainly determined by the neck geometry of the shake flask and to a lesser extent by the plug material and density.
In the autoclave, aluminium foil protects the cotton plugs from dripping water and should be removed shortly afterwards. If aluminium caps are used they should be fitted firmly onto the flask. When the caps move during the shaking operation, the gas exchange is not reproducible and there may be a greater risk of contamination because of the convective gas flow.
You can find more information about the mass transfer resistance of different sterile plugs in shaking bioreactors in the following publication:
«Mass transfer resistance of sterile plugs in shaking bioreactors»
Mrotzek, C., Anderlei, T., Henzler, H-J. und Büchs, J.:
Biochemical Engineering Journal (2001), Vol. 7 (2), pp 107 - 112