Let's start by saying that this is a mental model to help you better learn / think about these concepts, which means the usual aphorism applies: "All models are wrong, but some are useful" -- George Box.\
So if the difference between Network / Transport / Application levels are helpful to you, then great, but know that the boundaries are fuzzy and sometimes even wrong, so take it with a grain of salt.
Metaphor time!
I am trying to file my taxes by mail.
Network layer: The postal service.
I put my envelope into a mailbox, a guy picks it up, it goes to a sorting facility and is sorted based on the address on the envelope, it goes out for delivery, it makes it to the destination.
There are some security concerns that are unique to this transport layer; for example could a bad guy pull envelopes out of the mailbox? Could a malicious employee either at the sorting facility or on the delivery route do something bad to your envelope?
Transport layer: The envelope.
There's the sticky seal. There's the thickness of the paper of the envelope to prevent people reading the contents up against a light. There's the TO: and FROM: addresses on the envelope.
All of these things have potential security abuses associated with them. You could also think of security abuses that have to do with the interactions between the Network and Transport layers; for example messing with the stamp on the envelope or the shape of the envelope might cause it to get sorted differently, which could be abused.
Application layer: So your envelope gets successfully delivered to the government. They are going to open it and check that the forms inside are filled out properly. They will send you back mail based on whether they accepted your forms ore not.
There are security abuses unique to the application layer, like lying on the forms. You could also think of security abuses that have to do with the interactions between the Application and Transport layers, like writing someone else's From: address on the envelope to try to trick the government into processing the forms incorrectly or sending the response to the wrong place.
Summary: In all cases, a network communication involves two people trying to communicate over some network operated by a 3rd party. Security issues happen when someone can trick one of the parties involved to do something they shouldn't.
This is true in the physical world just as it is in the digital world.
Sometimes thinking of Network vs Transport vs Application will help you keep your thoughts straight, but beyond that there's not much use to models like that.