Question: * Holding A♣ 6⋄
* Flop K♣ 9♣ 6♣
* BB goes all in on Turn.

If I flop a club on Turn or River, pot is mine for sure. I call his all in, miss the flush, BB has two clubs and takes it. Should i have called his him?

Answer: 
You can think about the range of cards the villain could have that would make sense for him to push with, I'm assuming his all in is around pot size or less, overbets probably narrow villains range further:

Big drawing hands: 78 off, T8 with a club, 57 with a club, JQ with a club

Two pair hands: K9, 96s

Top pair: AK, KQ, KJ, AA

Sets: KK, 99, 66

Made flush hands: I've included all suited gap and double gap club connectors.

Air hands: How often will villain try and represent a flush/big draw?

Now you can take a lot of these out of his range if he's short stacked or a generally tight pre-flop player, and with information about how pre-flop went (was he given great odds to play preflop?)

Even with all of this range and without any bluffs, you are a favourite according to pokerstove. I suggest you play around with opponents hand ranges in pokerstove when analysing hands, and see how your holding plays against this.
If your opponent has the flush then you only have 7 outs so cannot call. 

If your opponent is doing this with a set or 2 pair then you can call.  

You have 14 outs and are right at 50% to hit by the river. 

You are at best 50% so I think you fold here.