For me I already get an error for func[[i]]:

In[20]:= func[x_] := x^2 + 2

In[21]:= func[[2]]

During evaluation of In[21]:= Part::partd: Part specification func[[2]] is longer than depth of object.

Out[21]= func[[2]]

So then the problem comes when using a List as the head of an expression. One way to make sure a message is issued for that case would be to define $Post:

In[22]:= list::notfunc = "Warning: list used as a function.";
$Post = ReplaceAll[x : (_List)[arg___] :> (Message[list::notfunc]; x)];

In[24]:= list = {1, 2, 3, 4};

In[25]:=list[3]

During evaluation of In[24]:= list::notfunc: Warning: list used as a function.

Out[25]= {1, 2, 3, 4}[3]