They were finally undone by Demba Ba's 68th-minute winner, which kept Chelsea two points behind league leaders Liverpool and Swansea still in relegation danger.
"If you go by the letter of the law it is a sending off, but if you do letter of the law every single game then you will get six or seven sendings off a game," Monk said.
"The disappointing thing was that he (referee Phil Dowd) looked like he signalled straight away 'no' - as if to signal it didn't warrant another yellow.
"Then their bench and manager surrounds the fourth official and their players surround the referee and then the red card comes later on.
"It makes you wonder, doesn't it?
"But I know Phil, and he is an honest guy
I don't think he responded to the pressure
If he says it was him giving himself time, then it is him giving himself time
But the circumstances make it strange.
"It's not great when people are asking for the ref to dish out a red card, but what can you do
It happens, and you trust that the ref was strong enough to deal with all that."
Assessing Flores' two cautions, Monk added: "I'm not disappointed in him, but he is an experienced pro and he should have used that experience in that situation.
"We have all been in that situation where you have been booked, and especially if it's early on, you are then treading on a tightrope for the rest of the game.
"The harshest punishment is getting sent off and Chico got sent off."
Swansea now head to Newcastle next Saturday, still needing probably one more win from their last four fixtures to retain their top-flight status.
"I've told the players that we have shown that desire and attitude not to be beaten," Monk said.
"Unfortunately, we have come away on a couple of occasions with nothing, but I've just said to them if we show exactly what we have done for the last four games then we will have no problems.
"We are not in a good position
We are not secure, and with four games left that's not the position you want to be in
It's in our hands, but we have to do something quickly and get something out of the next game."
Chelsea boss Jose Mourinho opted not to attend his post-match press conference, handing the job instead to assistant coach Steve Holland.
"Jose asked me to do it," Holland said, without offering any further explanation.
"It is something I have done a few times this year, and it is something I am more than happy to do it when he asks me."
On the Flores cautions, Holland added: "In my opinion, the two yellow card decisions were crystal clear.
"I have seen them both back, and I think the referee was quite clearly correct on both counts.
"I think the referee made the decision, and he made the decision correctly.
"As to who he speaks to and how long he takes over the decision, you would have to ask him how that works
For sure, ultimately he made the right decision.
"It (Swansea away) has always been a difficult fixture for us.
"They are a team that is very much based around keeping possession of the ball, and they can frustrate you for long periods because it is difficult to build pressure up against them.
"On the back of a Champions League game in midweek, which is emotionally, physically and mentally draining, you always worry about the impact that has on your next fixture.
"It is a fantastic three points for us, and very much a case of getting over the line, really."
Ba also scored the winner when Chelsea booked their Champions League semi-final place last Tuesday by knocking out Paris St Germain on away goals, and the title race is now hurtling towards a potential decider when Mourinho's team visit Anfield in two weeks' time.
"Not much has changed
We are five points clear of Manchester City, and they have two games more to play than us
If Manchester City win all their matches, they finish ahead of Chelsea," Holland said
"Obviously, it has been a good day for Liverpool, and it looks like being an exciting conclusion to the season.
"We have probably got to win all of our games, one way or another.
"That's the likelihood, but we have been facing that task now for a good couple of weeks, certainly on the back of our result at Crystal Palace
I think any leeway we had was eliminated after that result."
Source : PA
Source: PA