Any long-running series, especially in a crossover universe that involves time travel, can certainly run into some plot holes. The Flash, its writers have certainly done a great job in trying to patch up any narrative gaps that may unfold in the show.
The nature of a science fiction show like this, with the addition of the lore of the DC Universe, means that it's easy for the writing to get confused. Time travel, the Multiverse, hundreds of heroes and villains, and the connections to the much larger Arrowverse can all create plot holes; but what may seem like a story based issue can actually be explained away thanks to the clever writing of The Flash team.
Money Issues
While there are certainly times where strayed from realism, as is the case with any comic book property, a confusing aspect of the show has to be the way in which STAR Labs is funded. Indeed, it's often brushed aside that Team Flash shouldn't be able to afford any of their research.
However, a version of Wells actually creates a Flash Museum in STAR Labs, which presumably continues to bring in income. In addition, many of the team have side jobs and probably put in cash to the group; from their scientific research to their journalistic and detective careers.
Ralph's Changing Appearance
For season 7 Ralph Dibny had to be recast thanks to real-life controversies with the previous actor. The way that The Flash got around his change in appearance was by having Dibny stuck in an extreme explosion, which left his face unable to heal.
There was some confusion around this, though; why wouldn't Ralph go back to his normal appearance after he is healed, given that he can shapeshift? It seems that the scarring on that version of his face is permanent, though, which is the explanation for a new face.
Protecting Eddie Thawne
The Reverse-Flash is one of the deadliest villains to have ever been featured in the Arrowverse. In season 1 his reveal was quite an iconic moment, as was the fact that Eddie Thawne was secretly related to him all this time. One thing didn't add up though. Why would Eobard Thawne let his ancestor, Eddie, ever be in harm's way?
Eobard allowed Eddie to move to Central City (where his master plan takes place), become a police detective, and get involved with the Wests and the Allens. Eobard knew that Eddie's death would result in his own. Surely its a plot hole that he did not stop all this from happening? Well, his master plan likely predicted all of this; the one thing it did not foresee, thanks to his arrogance, was that Eddie would kill himself!
Caitlin's Powers
Caitlin Snow famously becomes Killer Frost in the comics as she does on the small screen. She developed her abilities after it was discovered she was a metahuman, thanks to the particle accelerator explosion. Powers don't normally make people evil, though.
For some reason, her abilities changed her personality, supposedly creating a plot hole. This isn't actually a plot hole at all though, as some time later it's revealed that her powers were with her at a much younger age, thanks to the experimentation of her father.
The Black Flash
The Black Flash is the CW's version of the Grim Reaper in many ways. This corrupted entity of the Speed Force tracks down any speedster that has misused their abilities and messed around with time. A number of villains have fallen to its undying wish to hunt them down.
However, Black Flash hasn't really gone after Barry despite the events of Flashpoint. It may be that this isn't a plot hole but rather something the Speed Force itself controlled. The Speed Force is trying to protect Barry and therefore doesn't want to send its Grim Reaper after him.
The Lack Of Superhero Help
Every time something major happens in the Flash's world the question is often asked, why hasn't he run to get help? He does so occasionally, with the Green Arrow being run in to help deal with varying situations and Supergirl flying by from time to time.
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It seems like a real flaw in the storytelling and while there are plenty of theories that try to explain it away, ultimately it isn't a plot hole but simply the fact that the other heroes are constantly busy. What's more, how is the Flash supposed to find them quick enough to run them into the danger zone? Time travel makes up an important part of the Flash mythos. The Scarlet Speedster is one of the few heroes in the Arrowverse who can actually travel through time, but the impact of his movements has extremely large consequences. In theory, there's a number of huge plot holes in regards to all of the time travel. However, the show has also demonstrated that there are explanations as to how some characters can still exist, which is largely impacted by the Multiverse as well as various time tricks that are difficult to understand. Ultimately, the time travel makes just enough sense. In Flash canon, Cisco originally created the Cold Gun so that if a speedster (or indeed the Flash) ever turned evil, they would have a weapon that was able to combat them. However, the Rogue Captain Cold stole the gun and another was never made. While this may seem odd considering the gun's purpose, the reason Cisco didn't make another was likely because they themselves found ways to combat the Cold Gun, demonstrating it wasn't actually that effective. The DCEU's link to the Arrowverse is quite confusing, but it really became mixed when the two Flash's met one another for the first time. Perhaps the DCEU is part of the wider Multiverse, but as Barry pointed out, this other Flash shouldn't have been able to cross over. It may seem like a plot hole that this never gets resolved but its actually part of a much larger ongoing mystery. It's actually quite possible that the film based on the Scarlet Speedster could offer up some answers and even have a second crossover! Harrison Wells has appeared time and time again in Team Flash's life in various ways. But there's never been a pure explanation as to why that is. It seems like a plot hole that for some reason the Wells would continue to be drawn to this Earth. It's not a plot hole, however, as many of the Wells were brought in by the team, while others were linked through coincidence. There's also clearly some kind of force in the Multiverse at play, drawing these characters in so they can continue to save the day.
All The Time Travel
No Duplicate Cold Gun
Existence Of The DCEU
Harrison Wells
