Data Model Limitations
NetBox is an extremely powerful tool for modeling network components and topologies. However, it doesn't (yet) support several fairly common complex scenarios which are difficult to model. This page seeks to compile such cases for reference and encourage exploration into potential solutions.
Physical Modeling
It's very common for certain lower-end branch or SMB network devices to make a logical interface available via one of two physical connections (typically twisted pair copper or SFP). For example, the Juniper ACX1100-AC provides a set of four copper and four SFP interfaces numbered 0/1/0 through 0/1/3: Each position can utilize either the copper port or its SFP peer, but not both.
These are difficult to model because it forces a layer of abstraction between the logical interface and its physical counterpart. Depending on the device, it might not even be possible to tell which physical port is in use.
The recommended approach in this case is to only model the physical interface that you intend to use, and simply ignore the existence of its alternate. While not a perfectly accurate, it's the solution most likely to avoid confusion and user error. (Be sure to designate the correct interface type when adding these interfaces to NetBox.)
Certain switch products, such as Cisco's Nexus series, can utilize physically separate switches as remote line cards (or "fabric extenders") of a parent device. These devices appear logically as line cards belonging to the switch, but are typically connected using regular Ethernet links and may physically reside far from the parent device. On top of this, such remote line cards are often connected to two parent devices, which share a common management plane.
This concept is difficult to model because it requires a layer of abstraction to treat the parent-to-child links differently from normal links.
The recommended approach is to create all of the parent and child devices as physical devices, and then create a virtual chassis to group them in NetBox as a single logical entity. You'll probably still want to create the physical connections between parents and children to ensure the cables are modeled appropriately, although currently there's no mechanism for designating these as intra-chassis links.