There may be a lot of bubbles in your transfering process

Thanks for your answer, but I think I need to make it more clear, this happens immediately after the etching of copper, at which point you can have an initial view of the whole graphene film, before any transfer process is carried out. 

Probably because of reverse reaction; did you flow methane or any other carbon precursors while cooling the chamber to RT? It is known that etching of graphene by hydrogen, i.e. the reverse reaction of the thermal decomposition of methane to graphene, may occur at elevated temperature. I think it is worthy to try flowing methane gas till the reaction chamber reaches down to room temperature.

i think  residual on copper foil bring out holes. maybe you can try some etching process for copper foil to remove residual before growing. I used Nitric acid to remove them.

I agree with all you have try all answer. before sample depostion the substrate surface must be carefully washes by H2SO4 then water many times and you can  polish it if it needs ,  and then dray it in any oven under vacuume. This can make big different.

I have experienced the same holes before, and it seems that they are originated basically due to the presence of reconstructed oxide particles during annealing stage. Try use another more purity copper, it may help you get rid off these holes