One mistake I've often seen made when planning for a software project or planning the road-map for a team is not taking into account the total cost of development. We often fall into the trap of planning our software based on one key data point; development effort. While development effort is likely the most volatile variable that goes into the cost of a project, it is by no means the only variable.
Planning isn't free
There are three major areas of planning that need to be accounted for when considering the true cost of a project. The first is in defining what the customer needs. This will involved someone (or multiple people) being the advocate for the customer. Likely this will involve a certain amount of research and a certain amount of customer interaction.
The second is in identifying upstream and downstream dependencies. Before you introduce change into your system, you need to understand how that change will affect people that depend on your system and on the systems you depend on. For instance, will your changes cause you to put more load on another system? Will they cause you to be able to handle less or more load on your existing system? Do they require your existing consumers to do additional work or is there work they can stop doing? It is likely that you will have to make some change in your system to account for these dependencies.
The last area is in defining key performance indicators. These are metrics that allow you to know if your software is working correctly or not. If you don't account for defining these then you won't be able to truly measure whether or not your software is successful.
System Architecture (or high level designs) aren't free
Often we think about a project start as the time when the developers start writing code. But this is incorrect. The old adage "measure twice and cut once" applies to software development as well. To build the right system, one that works for your customers, you need to have a solid design. True software costing accounts for the design and the time it takes to review the design.
I don't think I need to state the obvious, but I will for completeness. You need to account for the actual development effort in the total cost. Usually this is done in dev weeks. This could be one dev for 12 weeks or 3 devs for 4 weeks, depending on the parallelization that the project allows for.
Bug Fixes and Stabilization aren't free
Before you put any code into production you should be testing that code in a production like environment. Many teams have an integration or pre-prod environment which is built as a smaller scale replica of production. The very best teams have a way to drive production like traffic in this environment to help root out the bugs that seem to only be able to be found in production (like race conditions, threading issues, memory or other problems of scale).
Deploying Software isn't free
Hopefully by now your organization has started to, if not fully, embraced the DevOps movement. Irregardless of whether you have full continuous integration setup or a fully manual deployment there is some cost associated with the deployment of your code. In a fully automated environment it may be the cost of updating the automation. In a more manual deployment scenario it'll be the cost of validating and pushing the bits to production.
Maintenance and Operations isn't free
Once your software is in production, you have an implicit contract with your customers (if not explicit) to make sure that software is running. This involves routine maintenance as well as the operational cost associated with keeping the system running smoothly and responding well to changing usage patterns. Inevitably hardware fails, systems get more load than we expect, and bugs exist in the system that require intervention. Accounting for this cost is crucial in understanding the total cost of software development.
Documentation doesn't write itself
The last area that I want to call out is documentation. This is often forgotten about until it's too late. Your code should be as close to self documenting as possible, but your users will need a guide to the feature or the product. Don't forget to account for this in your costing.