The Alternate universe has produced a series of different, and entertaining Star Trek films. In the latest installment, the final frontier decides to "push back." Star Trek: Beyond is an undeniably well-done film with beautiful shots in space and on-surface alike. There are several points that had fans laughing, and crying alike.

RELATED: Top 10 Most Powerful Romulans In Star Trek, Ranked

However, there are points where the plot just feels off. How did our crew survive that? Does this align with the Prime Universe? These are the burning questions we're met with periodically throughout the film. Let's dive into the biggest plotholes of Star Trek: Beyond.

No Intruder Alert For Aliens In The Beginning

We all know the Alternate timeline to be different from the Prime universe in certain ways. However, one aspect that's seen some consistency is ship operations. The Enterprise's alert conditions have clearly remained the same, so why no "intruder alert" alarm when Kirk beamed back from the mediation with the Teenaxians?

At the beginning of Star Trek: Beyond, these little aliens maul Captain Kirk, and he frantically beams back aboard the Enterprise, unknowingly catching the little ones in the transporter beam with him. There was absolutely no concern from anyone. Perhaps they just considered them pests? The lack of an "intruder alert" leaves a hole right at the beginning of the story.

The Size And Design Of Yorktown Station

Yorktown Station is an undoubtedly beautiful addition to the movie. It's massive, likely meeting the size of a moon. It highlights the success of the Federation both in spatial design and in species diversity. There are, again, stark differences between the Prime and Alternate universes. A main one being the size and scope of Federation spacecraft.

The only issue here is the actual size of Yorktown Station, in comparison to the time in which it was built. We never see anything quite so grand in the Prime universe. It just seems a bit out there that the Federation is that much further along in this universe.

Uhura Spotting "Balthazar Edison" In The Video

The video highlights the driver of our villain. Aboard the Franklin, there was a video of the supposed crew on replay. The same shot was playing over and over again of the Franklin crew walking, talking, and laughing with each other. Once Uhura is aboard, she stops and analyzes the screen.

She plays it through roughly five times before slowing it down, and miraculously seeing a face that she couldn't before. Perhaps this could be accredited to futuristic Federation technology and a keen eye from Uhura. But it just seemed a little out there for their discovery of the Franklin captain's identity.

Motorcycle On The Franklin Working After So Long

First off, why is there a gas-powered vehicle on this starship? That point is feasible, but why does the PX90 work perfectly fine after so long? Kirk is happy to see a motorcycle resemblant to the one which his father owned. This point is revealed in the movie purely as an option for their distraction, which is poised later on as Kirk decides to launch a rescue mission for his crew.

RELATED: 10 Best Star Trek References In Pop Culture

The rescue, paired with Jaylah's holographic emitters and jelly wall technology (as well as some poor CGI), goes off without a hitch as the crew is beamed by the twenties onto the Franklin. Could it have been done without the motorcycle? Probably. Was it more interesting? We'll let you decide.

Scotty's Evacuation Via Photon Torpedo

When the Enterprise was being boarded and overwhelmed by enemy forces, Scotty's only choice was to abandon ship via a photon torpedo. Firstly, how did he remove the explosive components so quickly? Based on the shot from the movie, he was in the tube in like 45 seconds.

Second, torpedos launch quickly. This thing was moving when it launched from the Enterprise. He uses a remote controller to pilot the torpedo down to the planet's surface. The shot from the movie shows the torpedo colliding with the surface with brute force. The torpedo isn't designed to support or confine a human body inside. Realistically, Scotty should have died from whiplash.

Jaylah's Holographic Mobile Emitters

Jaylah had some pretty awesome tech down on the surface. She beat up a group of bandits all by herself. Well, in a sense. She beat the bandits by utilizing three holographic copies of herself—all with mobile emitters. Jumping to the Prime universe, in Star Trek: Voyager (which is over 100 years further along than where Beyond is at on the Kelvin timeline), The Doctor's mobile emitter wasn't discovered until later on in the show.

RELATED: 10 Unfair Star Trek vs Star Wars Comparisons

The Doctor's mobile emitter was salvaged from 29th Century technology, and everyone was a bit surprised that it existed. Now, we all know that there are differences between the two timelines. But this steep of a difference? Who knows? Maybe Jaylah is from the future.

Fixing The Franklin in 10 Minutes

Not long after the crew is back aboard the Franklin, we see the launching of an assault by Krall and his crew as they leave for Yorktown Station. So what does the Enterprise crew decide to do? Fix a really old starship to go defend Yorktown - which is perfectly reasonable, right? Well, they must've forgotten that their own starship (the best in the fleet) fell victim to Krall in about twenty minutes.

As the "bee" ships took off from the planet, the Enterprise crew worked at the Franklin. And they had the ship ready to go in maybe ten minutes, which just isn't feasible. At least they were ready to use minimal phase cannons to defend the snow globe of the Federation.

Using Music To Kill The "Bee" Ships

This idea wasn't a bad one, and it was clearly successful in the movie. The issue here is just how effective it was. Spock, aboard the Franklin, offers an idea to eliminate the threat of the "bee" ships. The Franklin would emit a signal on an unexpected frequency, which would disrupt their ability to communicate (and coordinate) with each other. The idea is perfectly logical and holds merit.

RELATED: Star Trek: 10 Hidden Details About Aliens Everyone Completely Missed

The only question is: Would this disruption make the ships explode immediately? Surely some ships would collide with each other, but other pilots might be able to maneuver on their own. The movie depicts them exploding upon "contact" with this signal in a rather over-the-top fashion. They did successfully protect Yorktown, but it was a bit far-fetched.

The Chase For Yorktown's Life Support Systems

Krall (Edison) makes it onto Yorktown Station. He, armed with the "Abronath," was to commit mass murder of all life on board. His plan was to reach this "hub" tied to the station's life support systems, where he would release this bio-weapon into the air supply. Kirk and the station's command room knew that quite quickly, so what did they do? They had Kirk pursue him on foot. Yes, you heard that correctly, on foot.

So we have millions of lives on the line, and Kirk is pursuing Krall on foot. Why didn't they use the transporter to beam Kirk to the hub, especially when Krall had a head start? No matter. Kirk made it on time and saved the day per usual. It just seems a bit illogical not to use all of the tools at your disposal.

Enterprise-A Construction In Yorktown Station

Okay, so the question on everyone's minds: Does Utopia Planitia not exist anymore? In the Prime universe, all starships we see are manufactured at the Utopia Planitia Shipyard at Mars. So why are they constructing the new Enterprise right in the middle of Yorktown? Is this where they're building all of the new starships? It just doesn't make any sense.

The final shot of the Enterprise-A is beautiful and highlights the continued journey of our beloved crew, something all fans were excited about. But realistically speaking, the shot should've been the Enterprise-A leaving from Mars (or at least a neutral location). At least their journey takes off near their previous borders to the unknown.

NEXT: Star Trek: 5 Characters We Want On Our Side In A Zombie Apocalypse (& 5 We Don’t)