Ok, here's a quick run-down of the problems I could find with the failing SMILES:
[CH2,$(CF2);R0][CH2,$(CF2);R0][CH2,$(CF2);R0][CH2,$(CF2);R0][CH2,$(CF2);R0][CH2,$(CF2);R0][CH2,$(CF2);R0][CH2,$(CF2);R0]
[F,Cl,Br,I,$(O(S(=O)(=O)))]-[CH,CH2;!$(CF2)]-[N,n]
[N,n,O,S;!$(S(=O)(=O))]-[CH,CH2;!$(CF2)][F,Cl,Br,I,$(O(S(=O)(=O)))]
These all contain "CF2" and that "2" is not legal. If you want -CF2 but not -CF3, then you need to do: "$(C(F)F);!$(C(F)(F)F)"
[[CH;!R];!$(C-N)]=C([$(S(=O)(=O)),$(C(F)(F)(F)),$(C#N),$(N(=O)(=O)),$([N+](=O)[O-]),$(C(=O))])([$(S(=O)(=O)),$(C(F)(F)(F)),$(C#N),$(N(=O)(=O)),$([N+](=O)[O-]),$(C(=O))])
This has a syntax error. I guess you mean:
[CH;!R;!$(C-N)]=C([$(S(=O)(=O)),$(C(F)(F)(F)),$(C#N),$(N(=O)(=O)),$([N+](=O)[O-]),$(C(=O))])([$(S(=O)(=O)),$(C(F)(F)(F)),$(C#N),$(N(=O)(=O)),$([N+](=O)[O-]),$(C(=O))])
[N,C,S,O]-&!@[N,C,S,O]&!@[N,C,S,O]&!@[N,C,S,O]&!@[N,C,S,O]&!@[N,C,S,O]&!@[N,C,S,O]
Not sure what you're trying to express with this one, but you need to have some kind of bond query before "&!@". If they should all be single bonds, this is:
[N,C,S,O]-&!@[N,C,S,O]-&!@[N,C,S,O]-&!@[N,C,S,O]-&!@[N,C,S,O]-&!@[N,C,S,O]-&!@[N,C,S,O]
ac-*=&!@*-&!@C(=O)&!@ca
Another missing bond query. I'm going to guess you meant:
[a]c-[*]=&!@[*]-&!@C(=O)-&!@c[a]
(I put the "a" and "*" in square brackets too, because I think it's clearer. It's not necessary)
c12cccc(C(=O)N(&!@C)C(=O)3)c2c3ccc1
Has a missing bond query.
([#6]OP(=O)(*)O[#6].[#6]OP(=O)(*)O[#6].[#6]OP(=O)(*)O[#6])
Too many parens. I guess you meant:
[#6]OP(=O)(*)O[#6].[#6]OP(=O)(*)O[#6].[#6]OP(=O)(*)O[#6]
*-C(=O)-&!@[NH]-C&!@C(=O)-&!@[NH]-*
missing bond query.
[#6,#7]&!@[#6](=&!@[CH])&!@C(=O)-&!@[C,N,O,S]
missing bond query
Si~O
"Si" needs to be in square brackets
For what it's worth, you should be getting error messages (not always easy to interpret, but there) in the console in KNIME for these problems.
-greg