So I was making a SkyTram (kind of like a Ski Lift, my DevForum post on it is here: Feedback On My SkyTram), and I was almost finished with it, until I saw this:
Hey you can call Tank and im here to help.
Have you tried using X-ray? This makes it so you can see through your object and you could try to select that part
Dear Logimite,
Here is a small guide from me that could help you on this problem and you might learn something new! Relax, take some drink and start reading.
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On the image above I moved the same face on Y axis and you can now clearly see what is the problem.
Here is how to fix this problem!
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I selected two edge loops, which would fix an issue on the other side as well. To select Edge Loops you hold Alt + Left Mouse Button Click or to select multiple Edge Loops you hold Shift + Alt + Left Mouse Button Click.
This is how you select Edge Loops and it will be very useful in your future projects.
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To switch between vertices, edges and faces, you can simply press 1 ; 2 ; 3 on your keyboard.
1 - Vert Selection
2 - Edge Selection
3 - Face Selection
In the next step I want to show you about another problem and how to fix it.
In Edit Mode I changed my selection to Vert Selection.
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Once Edge Loops are scaled to the middle point, I selected one vert on top.
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Then I moved it out on X Axis and here is a problem. Before this our faces were overlapping, now our verts are overlapping.
When two or more vertices are overlapping, this is named DOUBLES. You will always want to remove Doubles and have one vert at a place.
To do this I simply selected whole mesh in Edit Mode by pressing A.
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After that to remove Doubles, you will have to press a shortcut which depends on what version of Blender are you using.
In my case I am using 2.83 version of Blender.
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I pressed M to Merge and I will select By Distance.
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On the bottom of your Blender Interface, you will see that information popped up. It says that Blender has removed 9 vertice(s), which means that it worked.
Summary:
Our 2 Edge Loops had 18 vertices and when we scaled them together those vertices were overlapping each other. Now we simply merged them and now they are both connected!
Homework:
Homework file: Homework.blend (739.7 KB)
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I left the same problem on top of the Sky Lift to fix it by yourself after reading this guide. You will do the same steps as I did and this guide might be long, but once you figure it out, it’s actually 5 seconds of work.
**Additional Guide:**Auto - Smoothing Models
I want to also learn you how to Auto - Smooth properly. I feel like you know something about it, but I will post it for other viewers too.
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As you can see on the image above, edges here are not necessarily to be visible. They have to be smoothed out, in terms of style. Most modelers that begin with modeling think that this kind of issue is not necessary, which is wrong.
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To Shade Smooth a mesh, you select it in Object Mode and Right Mouse Button Click to open Object Context Menu. Select the Shade Smooth option. Once you are done with it, you will see really ugly shadows on your mesh, that will be fixed with Auto - Smooth option!
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Go to Object Data Properties on your right side of your screen which is indicated with green triangle icon.
Open Normals and check Auto Smooth option.
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I changed the angle on 50, so it automatically smoothens out some edges, while some edges are left sharp.
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This is how model looks currently.
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If I zoom in, I will see the sharp edge here. Why is it there though? You might already know the answer to this question, but here is why. You already marked some edges sharp to make them “stand out”. From my perspective this is not necessary at this spot.
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I will simply Clear Marked Sharp edges from here.
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To open Edge Menu, first enable Edge Selection. Go back to guide if you forgot how to! 
Once you did, you will select edges that are marked sharp!
Press Ctrl + E to open Edge Menu and select Clear Sharp option!
Go back to Object Mode.
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This is the final result of your model.
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I did a few changes and this is how your model looks finally.
Final Model File: Done.blend (777.5 KB)
I hope you and others learned something new from this guide! Have a great day! 
Regards,
DevAwesomely
Thanks a lot for this guide, its really gonna help me, especially the part where you explain how to remove the ugly shadows. 
Wow! Amazing response. This response helped me a lot. Can you please help me with this one error that happened?
So I wanted to make it more like this reference:
