Flores was dismissed on 16 minutes after picking up a second yellow card for a foul on Andre Schurrle after being booked for bringing down Willian just two minutes earlier.
Dowd did not immediately show a red card as Chelsea manager Jose Mourinho protested to the fourth official before Flores was eventually dismissed.
"That's the most disappointing thing for me," Monk told Sky Sports regarding the delay in Flores' red card. "He clearly said no, but I think he said he was biding his time.
"All you can see is their bench and manager in the fourth official's ear, then all of a sudden, our player is sent off where it looked like he wasn't going to do anything about it.
"That's the only question I have about it, but I'm sure he's got a legitimate answer."
Regarding the sending off itself, Monk said: "By the letter of the law, I guess it's a red card, but if you go by the letter of the law every week, you'll have seven or eight players sent off every game.
"It's one of them, but what can you do, you can't complain."
Monk was happy with Swansea's performance in adversity, but the defeat leaves his side just three points above the relegation zone with four games to play.
He continued: "We're not safe, we're clearly not safe and we're in desperate need of points.
"But I said to the players at the end not to walk out of the changing rooms disappointed after what they've given me today, and what they've given the fans, who were magnificent by the way.
"It was a real lift and we needed a reaction from Hull. We didn't get the result we wanted, or the points we probably deserved, but if we take that attitude and desire into the last four games I'm pretty sure we'll be fine."
Monk also confirmed that his opposite number Mourinho did not shake hands at the final whistle, saying: "I turned round and he decided to go straight in.
"I never spoke to him throughout the game, so you'll have to ask him, but I'm not really [disappointed]."