Marc Williams, after scoring Wales' goals, was sent off along with Craig Davies.
"Both dismissals were when the ball was out of play, they were for retaliation - and the lads have said they were punched," said Bryan Flynn.
"I didn't have a clear view of what happened, but we will look at both incidents when we have all the evidence and have seen the referee's report, before deciding whether we will appeal or take the situation further.
"But it's fair to say that retaliation gets you nowhere. When you play at this level you must have international level self discipline, you have to maintain those standards whatever happens to you.
"I would expect Turkey to be too good for Israel, but then we will have to beat them, and that will be tough.
"But we can produce a top-level performance when Turkey come to Ninian Park, and it could all go down to goal difference."
Wales must hope that Turkey beat Israel and then Wales get a decent victory over Turkey to have any chance of progressing.